Quantitative time-resolved measurement of membrane protein-ligand interactions using microcantilever array sensors

Midinfrared Spectroscopic Analysis of Aqueous Mixtures Using Artificial-Intelligence-Enhanced Metamaterial Waveguide Sensing Platform

As miniaturized solutions, mid-infrared (MIR) waveguide sensors are promising for label-free compositional detection of mixtures leveraging plentiful absorption fingerprints. However, the quantitative analysis of liquid mixtures is still challenging using MIR waveguide sensors, as the absorption spectrum overlaps for multiple organic components accompanied by strong water absorption background. Here, we present an artificial-intelligence-enhanced metamaterial waveguide sensing platform (AIMWSP) for aqueous mixture analysis in the MIR. With the sensitivity-improved metamaterial waveguide and assistance of machine learning, the MIR absorption spectra of a ternary mixture in water can be successfully distinguished and decomposed to single-component spectra for predicting concentration. A classification accuracy of 98.88% for 64 mixing ratios and 92.86% for four concentrations below the limit of detection (972 ppm, based on 3σ) with steps of 300 ppm are realized. Besides, the mixture concentration prediction with root-mean-squared error varying from 0.107 vol % to 1.436 vol % is also achieved. Our work indicates the potential of further extending this sensing platform to MIR spectrometer-on-chip aiming for the data analytics of multiple organic components in aqueous environments.

Rapid Bacteria Detection from Patients' Blood Bypassing Classical Bacterial Culturing

Sepsis is a life-threatening condition mostly caused by a bacterial infection resulting in inflammatory reaction and organ dysfunction if not treated effectively. Rapid identification of the causing bacterial pathogen already in the early stage of bacteremia is therefore vital. Current technologies still rely on time-consuming procedures including bacterial culturing up to 72 h. Our approach is based on ultra-rapid and highly sensitive nanomechanical sensor arrays. In measurements we observe two clearly distinguishable distributions consisting of samples with bacteria and without bacteria respectively. Compressive surface stress indicates the presence of bacteria. For this proof-of-concept, we extracted total RNA from EDTA whole blood samples from patients with blood-culture-confirmed bacteremia, which is the reference standard in diagnostics. We determined the presence or absence of bacterial RNA in the sample through 16S-rRNA hybridization and species-specific probes using nanomechanical sensor arrays. Via both probes, we identified two clinically highly-relevant bacterial species i.e., Escherichia coli and Staphylococcus aureus down to an equivalent of 20 CFU per milliliter EDTA whole blood. The dynamic range of three orders of magnitude covers most clinical cases. We correctly identified all patient samples regarding the presence or absence of bacteria. We envision our technology as an important contribution to early and sensitive sepsis diagnosis directly from blood without requirement for cultivation. This would be a game changer in diagnostics, as no commercial PCR or POCT device currently exists who can do this.

Lifting the Veil: Characteristics, Clinical Significance, and Application of β-2-Microglobulin as Biomarkers and Its Detection with Biosensors

Because β-2-microglobulin (β₂M) is a surface protein that is present on most nucleated cells, it plays a key role in the human immune system and the kidney glomeruli to regulate homeostasis. The primary clinical significance of β₂M is in dialysis-related amyloidosis, a complication of end-stage renal disease caused by a gradual accumulation of β₂M in the blood. Therefore, the function of β₂M in kidney-related diseases has been extensively studied to evaluate its glomerular and tubular functions. Because increased β₂M shedding due to rapid cell turnover may indicate other underlying medical conditions, the possibility to use β₂M as a versatile biomarker rose in prominence across multiple disciplines for various applications. Therefore, this work has reviewed the recent use of β₂M to detect various diseases and its progress as a biomarker. While the use of state-of-the-art β₂M detection requires sophisticated tools, high maintenance, and labor cost, this work also has reported the use of biosensor to quantify β₂M over the past decade. It is hoped that a portable and highly efficient β₂M biosensor device will soon be incorporated in point-of-care testing to provide safe, rapid, and reliable test results.

Living Sample Viability Measurement Methods from Traditional Assays to Nanomotion

Living sample viability measurement is an extremely common process in medical, pharmaceutical, and biological fields, especially drug pharmacology and toxicology detection. Nowadays, there are a number of chemical, optical, and mechanical methods that have been developed in response to the growing demand for simple, rapid, accurate, and reliable real-time living sample viability assessment. In parallel, the development trend of viability measurement methods (VMMs) has increasingly shifted from traditional assays towards the innovative atomic force microscope (AFM) oscillating sensor method (referred to as nanomotion), which takes advantage of the adhesion of living samples to an oscillating surface. Herein, we provide a comprehensive review of the common VMMs, laying emphasis on their benefits and drawbacks, as well as evaluating the potential utility of VMMs. In addition, we discuss the nanomotion technique, focusing on its applications, sample attachment protocols, and result display methods. Furthermore, the challenges and future perspectives on nanomotion are commented on, mainly emphasizing scientific restrictions and development orientations.

Real-Time Sensing with Multiplexed Optomechanical Resonators

Nanoelectromechanical resonators have been successfully used for a variety of sensing applications. Their extreme resolution comes from their small size, which strongly limits their capture area. This leads to a long analysis time and the requirement for large sample quantity. Moreover, the efficiency of the electrical transductions commonly used for silicon resonators degrades with increasing frequency, limiting the achievable mechanical bandwidth and throughput. Multiplexing a large number of high-frequency resonators appears to be a solution, but this is complex with electrical transductions. We propose here a route to solve these issues, with a multiplexing scheme for very high-frequency optomechanical resonators. We demonstrate the simultaneous frequency measurement of three silicon microdisks fabricated with a 200 mm wafer large-scale process. The readout architecture is simple and does not degrade the sensing resolutions. This paves the way toward the realization of sensors for multiparametric analysis with an extremely low limit of detection and response time.

Fabricating Silicon Resonators for Analysing Biological Samples

The adaptability of microscale devices allows microtechnologies to be used for a wide range of applications. Biology and medicine are among those fields that, in recent decades, have applied microtechnologies to achieve new and improved functionality. However, despite their ability to achieve assay sensitivities that rival or exceed conventional standards, silicon-based microelectromechanical systems remain underutilised for biological and biomedical applications. Although microelectromechanical resonators and actuators do not always exhibit optimal performance in liquid due to electrical double layer formation and high damping, these issues have been solved with some innovative fabrication processes or alternative experimental approaches. This paper focuses on several examples of silicon-based resonating devices with a brief look at their fundamental sensing elements and key fabrication steps, as well as current and potential biological/biomedical applications.

Quantitative epitope analysis reveals drastic 63% reduced immuno-affinity and 60% enhanced transmissibility for SARS-CoV-2 variants

SARS-CoV-2 is the cause of a global pandemic that has led to more than 4 million deaths, continues to spread and holds the world in a tight grip. The virus has developed substantial mutations that undermine the efficacy of current vaccines and monoclonal antibody therapies. Semi-quantitative immuno - and neutralization assays are unable to provide direct quantitative insights about the minute variations of emerging mutants. Here, we develop a quantitative assay that enables synchronous screening of emerging variant epitopes with single amino acid resolution. We report on specific label-free quantitative nanomechanical analysis of pseudovirus spike interaction with ACE2 receptors. Within minutes, we can characterize the B.1.1.7 variant transmissibility due to its 63% increased binding, and measure a 60% reduced efficacy of antibodies towards B.1.351 and P.1 variants. Our technology can assist vaccine development studies, with focus on comparing protection patterns and novel vaccine candidates and tracking of immunity over time.

Interactive Effects of Biosynthesized Nanocomposites and Their Antimicrobial and Cytotoxic Potentials

The present study investigated the biosynthesis of silver (AgNPs), zinc oxide (ZnONPs) and titanium dioxide (TiO2NPs) nanoparticles using Aspergillusoryzae, Aspergillusterreus and Fusariumoxysporum. Nanocomposites (NCs) were successfully synthesized by mixing nanoparticles using a Sonic Vibra-Cell VC/VCX processor. A number of analytical techniques were used to characterize the synthesized biological metal nanoparticles. Several experiments tested biologically synthesized metal nanoparticles and nanocomposites against two types of human pathogenic bacteria, including Gram-positive Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA), and Gram-negative Escherichia coli and Pseudomonasaeruginosa. Additionally, the antitumor activity in HCT-116 cells (colonic carcinoma) was also evaluated. Significant antimicrobial effects of various synthesized forms of nanoparticles and nanocomposites against E. coli and P. aeruginosa bacteria were detected. Various synthesized biogenic forms of nanoparticles and nanocomposite (9.0 to 29 mm in diameter) had high antibacterial activity and high antitumor activity against HCT-116 cells (colonic carcinoma) with IC50 values of 0.7-100 µg/mL. Biosynthesized NPs are considered an alternative to large-scale biosynthesized metallic nanoparticles and nanocomposites, are simple and cost effective, and provide stable nanomaterials.

Nanomotion Detection-Based Rapid Antibiotic Susceptibility Testing

Rapid antibiotic susceptibility testing (AST) could play a major role in fighting multidrug-resistant bacteria. Recently, it was discovered that all living organisms oscillate in the range of nanometers and that these oscillations, referred to as nanomotion, stop as soon the organism dies. This finding led to the development of rapid AST techniques based on the monitoring of these oscillations upon exposure to antibiotics. In this review, we explain the working principle of this novel technique, compare the method with current ASTs, explore its application and give some advice about its implementation. As an illustrative example, we present the application of the technique to the slowly growing and pathogenic Bordetella pertussis bacteria.

Nanotechnological immunoassay for rapid label-free analysis of candidate malaria vaccines

Malaria is a life-threatening epidemic disease with half of the world's population at risk. Although its incidence rate has fallen since 2010, this ratio dramatically stalled between 2014 and 2018. New fast and optimized tools in vaccine analysis and seroconversion testing are critically needed. We developed a clinical diagnostic device based on piezo-actuated nanoresonators that perform as quantitative in situ calibrated nano-bio sensors for specific detection of multiple target molecules in serum samples. The immunoassay successfully diagnoses humoral immune responses induced by malaria vaccine candidates and reveals the timeline and stage of the infection. We applied the newly developed strategy to a variety of different samples, from pure antibody/vaccine solutions, to blood samples from clinical trials on both naïve and pre-exposed malaria volunteers from sub-Saharan countries. Our nanomechanical assay provides a direct one-step label-free quantitative immunoassay that is on par with the gold-standard, multi-step enzyme-linked immunosorbent assay (ELISA). We achieve a limit of detection of few pg ml-1, or sub-pM concentrations. The 6 μl sample volume allows more than 50 experiments from one finger prick. Furthermore, we simultaneously detected multiple analytes by differential functionalization of multiple sensors in parallel. The inherent differential read-out with in situ controls reduces false positive results. Due to the faster turnaround time, the minimal volume required and the automatized handling system, this technique has great potential for miniaturization and routine diagnostics in pandemic emergencies.

Rapid and Ultrasensitive Detection of Mutations and Genes Relevant to Antimicrobial Resistance in Bacteria

The worldwide emergence of multidrug-resistant (MDR) bacteria is associated with significant morbidity, mortality, and healthcare costs. Rapid and accurate diagnostic methods to detect antibiotic resistance are critical for antibiotic stewardship and infection control measurements. Here a cantilever nanosensor-based diagnostic assay is shown to detect single nucleotide polymorphisms (SNPs) and genes associated with antibiotic resistance in Gram negative (Pseudomonas aeruginosa) and positive (Enterococcus faecium) bacteria, representing frequent causes for MDR infections. Highly specific RNA capture probes for SNPs (ampRD135G or ampRG154R ) or resistance genes (vanA, vanB, and vanD) allow to detect the binding of bacterial RNA within less than 5 min. Serial dilutions of bacterial RNA indicate an unprecedented sensitivity of 10 fg µL-1 total RNA corresponding to less than ten bacterial cells for SNPs and 1 fg µL-1 total RNA for vanD detection equivalent to single bacterial cell sensitivity.

Rapid and sensitive detection of cardiac troponin I using a force enhanced immunoassay with nanoporous membrane

There is a need for point of care diagnostic technologies that are rapid, sensitive, easy to use, and relatively inexpensive. In this article we describe an assay that uses an antibody functionalized nanoporous membrane and superparamagnetic beads to capture and detect human cardiac troponin I (cTnI), which is an important biomarker for acute myocardial infarction (AMI). The membrane assisted force differentiation assay (mFDA) is capable of detecting cTnI at a sensitivity of 0.1 pg ml^-1 in 15% serum in less than 16 minutes, which is a significant improvement in performance over conventional lateral flow immuosorbant assays. The speed of this assay results from the rapid concentration of cTnI on the surface of the nanoporous membrane and the use of the magnetic beads to react with the analyte, which rapidly react with the immobilized cTnI. The increased sensitivity of assay results from the use of magnetically controlled forces that reduce the nonspecific background and modify both the on-rate and off-rate. We believe that the improved performance and ease of application of the mFDA will make it useful in the early identification of AMI as well as other diseases based on the detection of 1 pg ml^-1 variations in the concentrations cTnI in blood.

A perspective view on the nanomotion detection of living organisms and its features

The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tools to monitor the response of single cells to chemical or pharmaceutical stimuli. Recently, it has been demonstrated that all living organisms oscillate at a nanometric scale and that these oscillations stop as soon as the organisms die. These nanometric scale oscillations can be detected by depositing living cells onto a micro-fabricated cantilever and by monitoring its displacements with an atomic force microscope-based electronics. Such devices, named nanomotion sensors, have been employed to determine the resistance profiles of life-threatening bacteria within minutes, to evaluate, among others, the effect of chemicals on yeast, neurons, and cancer cells. The data obtained so far demonstrate the advantages of nanomotion sensing devices in rapidly characterizing microorganism susceptibility to pharmaceutical agents. Here, we review the key aspects of this technique, presenting its major applications. and detailing its working protocols.

Nanomotion detection based on atomic force microscopy cantilevers

Atomic force microscopes (AFM) or low-noise in-house dedicated devices can highlight nanomotion oscillations. The method consists of attaching the organism of interest onto a silicon-based sensor and following its nano-scale motion as a function of time. The nanometric scale oscillations exerted by biological specimens last as long the organism is viable and reflect the status of the microorganism metabolism upon exposure to different chemical or physical stimuli. During the last couple of years, the nanomotion pattern of several types of bacteria, yeasts and mammalian cells has been determined. This article reviews this technique in details, presents results obtained with dozens of different microorganisms and discusses the potential applications of nanomotion in fundamental research, medical microbiology and space exploration.

Simultaneous and Ultrasensitive Detection of Foodborne Bacteria by Gold Nanoparticles-Amplified Microcantilever Array Biosensor

Foodborne pathogens, especially bacteria, are explicitly threatening public health worldwide. Biosensors represent advances in rapid diagnosis with high sensitivity and selectivity. However, multiplexed analysis and minimal pretreatment are still challenging. We fabricate a gold nanoparticle (Au NP)-amplified microcantilever array biosensor that is capable of determining ultralow concentrations of foodborne bacteria including Escherichia coli O157:H7, Vibrio parahaemolyticus, Salmonella, Staphylococcus aureus, Listeria monocytogenes, Shigella, etc. The method is much faster than using conventional tools without germiculturing and PCR amplification. The six pairs of ssDNA probes (ssDNA₁ + ssDNA₂ partially complementary to the target gene) that originated from the sequence analysis of the specific gene of the bacteria were developed and validated. The ssDNA₁ probes were modified with -S-(CH₂)₆ at the 5′-end and ready to immobilize on the self-assembled monolayers (SAMs) of the sensing cantilevers in the array and couple with Au NPs, while 6-mercapto-1-hexanol SAM modification was carried out on the reference cantilevers to eliminate the interferences by detecting the deflection from the environment induced by non-specific interactions. For multianalyte sensing, the target gene sequence was captured by the ssDNA₂-Au NPs in the solution, and then the Au NPs-ssDNA₂-target complex was hybridized with ssNDA₁ fixed on the beam of the cantilever sensor, which results in a secondary cascade amplification effect. Integrated with the enrichment of the Au NP platform and the microcantilever array sensor detection, multiple bacteria could be rapidly and accurately determined as low as 1–9 cells/mL, and the working ranges were three to four orders of magnitude. There was virtually no cross-reaction among the various probes with different species. As described herein, it holds great potential for rapid, multiplexed, and ultrasensitive detection in food, environment, clinical, and communal samples.

Biomimetic Membranes with Transmembrane Proteins: State-of-the-Art in Transmembrane Protein Applications

In biological cells, membrane proteins are the most crucial component for the maintenance of cell physiology and processes, including ion transportation, cell signaling, cell adhesion, and recognition of signal molecules. Therefore, researchers have proposed a number of membrane platforms to mimic the biological cell environment for transmembrane protein incorporation. The performance and selectivity of these transmembrane proteins based biomimetic platforms are far superior to those of traditional material platforms, but their lack of stability and scalability rule out their commercial presence. This review highlights the development of transmembrane protein-based biomimetic platforms for four major applications, which are biosensors, molecular interaction studies, energy harvesting, and water purification. We summarize the fundamental principles and recent progress in transmembrane protein biomimetic platforms for each application, discuss their limitations, and present future outlooks for industrial implementation.

Surface Area Enhancement of Nanomechanical Disk Resonators Using MWCNT for Mass-Sensing Applications

This work presents fabrication of thermal-piezoresistive nanoelectromechanical silicon disk resonators and their characterization as highly sensitive mass sensors. Forest of multiwall carbon nanotubes (MWCNTs) has been grown on the top surface of the fabricated devices, increasing the resonator effective surface area, which, in turn, increases the adsorption capacity and, therefore, the frequency shift of the sensor in molecular or particulate detection applications. To investigate the effect of the enhanced surface area on frequency shift, devices with and without MWCNTs were exposed to an aqueous solution of manganese sulfate for different deposition times and the resonance frequency shift was recorded accordingly. The measured frequency shift for the devices covered with MWCNTs was 14× higher than similar bare silicon devices. Furthermore, mass loading experiments were performed using gold nanoparticles as the loading mass. A novel way to attach gold nanoparticles on the carbon nanotubes (CNTs) wall was developed here. Oxygen plasma treatment introduced dangling bonds on the MWCNTs walls to facilitate the bonding between them and trimethoxysilane aldehyde molecules, forming the self-assembled monolayer (SAM). After functionalization of the device with SAM and antiinfluenza H1N1 viruses (AB), the device was exposed to a solution of Antimouse IgG (whole molecule)-gold antibody produced in goat products. The results showed more than three times response enhancement for the resonators with MWCNTs.

A Rapid Unraveling of the Activity and Antibiotic Susceptibility of Mycobacteria

The development of antibiotic-resistant bacteria is a worldwide health-related emergency that calls for new tools to study the bacterial metabolism and to obtain fast diagnoses. Indeed, the conventional analysis time scale is too long and affects our ability to fight infections. Slowly growing bacteria represent a bigger challenge, since their analysis may require up to months. Among these bacteria, Mycobacterium tuberculosis, the causative agent of tuberculosis, has caused more than 10 million new cases and 1.7 million deaths in 2016 only. We employed a particularly powerful nanomechanical oscillator, the nanomotion sensor, to characterize rapidly and in real time tuberculous and nontuberculous bacterial species, Mycobacterium bovis bacillus Calmette-Guérin and Mycobacterium abscessus, respectively, exposed to different antibiotics. Here, we show how high-speed and high-sensitivity detectors, the nanomotion sensors, can provide a rapid and reliable analysis of different mycobacterial species, obtaining qualitative and quantitative information on their responses to different drugs. This is the first application of the technique to tackle the urgent medical issue of mycobacterial infections, evaluating the dynamic response of bacteria to different antimicrobial families and the role of the replication rate in the resulting nanomotion pattern. In addition to a fast analysis, which could massively benefit patients and the overall health care system, we investigated the real-time responses of the bacteria to extract unique information on the bacterial mechanisms triggered in response to antibacterial pressure, with consequences both at the clinical level and at the microbiological level.

Experimental Setup for Dynamic Analysis of Micro- and Nano-Mechanical Systems in Vacuum, Gas, and Liquid

An experimental setup to perform dynamic analysis of a micro- and nano-mechanical system in vacuum, gas, and liquid is presented. The setup mainly consists of a piezoelectric excitation part and the chamber that can be either evacuated for vacuum, or filled with gas or water. The design of the piezoelectric actuator was based on a Langevin transducer. The chamber is made out of materials that can sustain: vacuum, variety of gases and different types of liquids (mild acids, alkalies, common alcohols and oils). All the experiments were performed on commercial cantilevers used for contact and tapping mode Atomic Force Microscopy (AFM) with stiffness 0.2 N/m and 48 N/m, respectively, in vacuum, air and water. The performance of the setup was evaluated by comparing the measured actuator response to a finite element model. The frequency responses of the two AFM cantilevers measured were compared to analytical equations. A vacuum level of 0.6 mbar was obtained. The setup has a bandwidth of 10⁻550 kHz in vacuum and air, and a bandwidth of 50⁻550 kHz in liquid. The dynamic responses of the cantilevers show good agreement with theory in all media.

Modified cantilever arrays improve sensitivity and reproducibility of nanomechanical sensing in living cells

Mechanical signaling involved in molecular interactions lies at the heart of materials science and biological systems, but the mechanisms involved are poorly understood. Here we use nanomechanical sensors and intact human cells to provide unique insights into the signaling pathways of connectivity networks, which deliver the ability to probe cells to produce biologically relevant, quantifiable and reproducible signals. We quantify the mechanical signals from malignant cancer cells, with 10 cells per ml in 1000-fold excess of non-neoplastic human epithelial cells. Moreover, we demonstrate that a direct link between cells and molecules creates a continuous connectivity which acts like a percolating network to propagate mechanical forces over both short and long length-scales. The findings provide mechanistic insights into how cancer cells interact with one another and with their microenvironments, enabling them to invade the surrounding tissues. Further, with this system it is possible to understand how cancer clusters are able to co-ordinate their migration through narrow blood capillaries.

Samadhan Patil et al. report a new method for improving the sensitivity and reproducibility of mechanobiological measurements in malignant cancer cells. Their findings provide insight into the interaction of cells with each other and the microenvironment and may impact our understanding of metastasis.

Analysis of Multiplexed Nanosensor Arrays Based on Near-Infrared Fluorescent Single-Walled Carbon Nanotubes

The high-throughput, label-free detection of biomolecules remains an important challenge in analytical chemistry with the potential of nanosensors to significantly increase the ability to multiplex such assays. In this work, we develop an optical sensor array, printable from a single-walled carbon nanotube/chitosan ink and functionalized to enable a divalent ion-based proximity quenching mechanism for transducing binding between a capture protein or an antibody with the target analyte. Arrays of 5 × 6, 200 μm near-infrared (nIR) spots at a density of ≈300 spots/cm² are conjugated with immunoglobulin-binding proteins (proteins A, G, and L) for the detection of human IgG, mouse IgM, rat IgG2a, and human IgD. Binding kinetics are measured in a parallel, multiplexed fashion from each sensor spot using a custom laser scanning imaging configuration with an nIR photomultiplier tube detector. These arrays are used to examine cross-reactivity, competitive and nonspecific binding of analyte mixtures. We find that protein G and protein L functionalized sensors report selective responses to mouse IgM on the latter, as anticipated. Optically addressable platforms such as the one examined in this work have potential to significantly advance the real-time, multiplexed biomolecular detection of complex mixtures.

The Role of Nanomechanics in Healthcare

Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.

Acoustic biosensors

Resonant and acoustic wave devices have been researched for several decades for application in the gravimetric sensing of a variety of biological and chemical analytes. These devices operate by coupling the measurand (e.g. analyte adsorption) as a modulation in the physical properties of the acoustic wave (e.g. resonant frequency, acoustic velocity, dissipation) that can then be correlated with the amount of adsorbed analyte. These devices can also be miniaturized with advantages in terms of cost, size and scalability, as well as potential additional features including integration with microfluidics and electronics, scaled sensitivities associated with smaller dimensions and higher operational frequencies, the ability to multiplex detection across arrays of hundreds of devices embedded in a single chip, increased throughput and the ability to interrogate a wider range of modes including within the same device. Additionally, device fabrication is often compatible with semiconductor volume batch manufacturing techniques enabling cost scalability and a high degree of precision and reproducibility in the manufacturing process. Integration with microfluidics handling also enables suitable sample pre-processing/separation/purification/amplification steps that could improve selectivity and the overall signal-to-noise ratio. Three device types are reviewed here: (i) bulk acoustic wave sensors, (ii) surface acoustic wave sensors, and (iii) micro/nano-electromechanical system (MEMS/NEMS) sensors.

Rapid Prototyping of Chemical Microsensors Based on Molecularly Imprinted Polymers Synthesized by Two-Photon Stereolithography

Two-photon stereolithography is used for rapid prototyping of submicrometre molecularly imprinted polymer-based 3D structures. The structures are evaluated as chemical sensing elements and their specific recognition properties for target molecules are confirmed. The 3D design capability is exploited and highlighted through the fabrication of an all-organic molecularly imprinted polymeric microelectromechanical sensor.

Highly sensitive ligand-binding assays in pre-clinical and clinical applications: immuno-PCR and other emerging techniques

Recombinant DNA technology and corresponding innovations in molecular biology, chemistry and medicine have led to novel therapeutic biomacromolecules as lead candidates in the pharmaceutical drug development pipelines. While monoclonal antibodies and other proteins provide therapeutic potential beyond the possibilities of small molecule drugs, the concomitant demand for supportive bioanalytical sample testing creates multiple novel challenges. For example, intact macromolecules can usually not be quantified by mass-spectrometry without enzymatic digestion and isotopically labeled internal standards are costly and/or difficult to prepare. Classical ELISA-type immunoassays, on the other hand, often lack the sensitivity required to obtain pharmacokinetics of low dosed drugs or pharmacodynamics of suitable biomarkers. Here we summarize emerging state-of-the-art ligand-binding assay technologies for pharmaceutical sample testing, which reveal enhanced analytical sensitivity over classical ELISA formats. We focus on immuno-PCR, which combines antibody specificity with the extremely sensitive detection of a tethered DNA marker by quantitative PCR, and alternative nucleic acid-based technologies as well as methods based on electrochemiluminescence or single-molecule counting. Using case studies, we discuss advantages and drawbacks of these methods for preclinical and clinical sample testing.

Finite Element Analysis on Nanomechanical Detection of Small Particles: Toward Virus Detection

Detection of small particles, including viruses and particulate matter (PM), has been attracting much attention in light of increasing need for environmental monitoring. Owing to their high versatility, a nanomechanical sensor is one of the most promising sensors which can be adapted to various monitoring systems. In this study, we present an optimization strategy to efficiently detect small particles with nanomechanical sensors. Adsorption of particles on the receptor layer of nanomechanical sensors and the resultant signal are analyzed using finite element analysis (FEA). We investigate the effect of structural parameters (e.g., adsorption position and embedded depth of a particle and thickness of the receptor layer) and elastic properties of the receptor layer (e.g., Young's modulus and Poisson's ratio) on the sensitivity. It is found that a membrane-type surface stress sensors (MSS) has the potential for robust detection of small particles.

Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing

RNA splicing plays important roles in transcriptome and proteome diversity. Herein, we describe the use of a nanoplasmonic system that unveils RNA folding and assembly during pre-mRNA splicing wherein the quantification of mRNA splice variants is not taken into account. With a couple of SERS-probes and plasmonic probes binding at the boundary sites of exon-2/intron-2 and intron-2/exon-3 of the pre-mature RNA of the β-globin gene, the splicing process brings the probes into the plasmonic bands. For plasmonic probes, a plasmon shift increase of ∼29 nm, corresponding to intron removal and exon-2 and exon-3 connection to form the mRNA molecule, is measured by plasmonic coupling. The increased scattering intensity and surface-enhanced Raman scattering (SERS) fingerprinting reveal the clear dynamics of pre-mRNA splicing. Moreover, a time-resolved experiment of individual RNA molecules exhibited a successful splicing and an inhibited splicing event by 33 μM biflavonoid isoginkgetin, a general inhibitor of RNA splicing. The results suggest that the RNA splicing is successfully monitored with the nanoplasmonic system. Thus, this platform can be useful for studying RNA nanotechnology, biomolecular folding, alternative splicing, and maturation of microRNA.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Nanomechanical Sensors

This chapter introduces nanomechanical sensors and their applications. All molecules have “volume” and “mass.” Direct measurement of these fundamental parameters can realize label-free and real-time measurements. Nanomechanical sensors have been emerging as a key device for such label-free and real-time measurements with their multiple operation modes; static and dynamic modes for detecting volume- and mass-related features, respectively. A cantilever array sensor is a representative example among various geometries, while structural optimization can enhance the scope of nanomechanical sensors in both academic and industrial applications. One of the most advanced sensing platforms is a membrane-type surface stress sensor (MSS), which realizes both high sensitivity and compact system at the same time. The MSS is also expected to contribute to addressing nanomechanical behavior of living cells and their network.

Toward Higher-Order Mass Detection: Influence of an Adsorbate's Rotational Inertia and Eccentricity on the Resonant Response of a Bernoulli-Euler Cantilever Beam

In this paper a new theoretical model is derived, the results of which permit a detailed examination of how the resonant characteristics of a cantilever are influenced by a particle (adsorbate) attached at an arbitrary position along the beam’s length. Unlike most previous work, the particle need not be small in mass or dimension relative to the beam, and the adsorbate’s geometric characteristics are incorporated into the model via its rotational inertia and eccentricity relative to the beam axis. For the special case in which the adsorbate’s (translational) mass is indeed small, an analytical solution is obtained for the particle-induced resonant frequency shift of an arbitrary flexural mode, including the effects of rotational inertia and eccentricity. This solution is shown to possess the exact first-order behavior in the normalized particle mass and represents a generalization of analytical solutions derived by others in earlier studies. The results suggest the potential for “higher-order” nanobeam-based mass detection methods by which the multi-mode frequency response reflects not only the adsorbate’s mass but also important geometric data related to its size, shape, or orientation (i.e., the mass distribution), thus resulting in more highly discriminatory techniques for discrete-mass sensing.

An optimised silicon piezoresistive microcantilever sensor for surface stress studies

Surface stress is a versatile and efficient means to study various physical, chemical, biochemical and biological processes. This work focuses on developing high sensitive piezoresistive microcantilever designs to study surface stress. The cantilevers are made of silicon with rectangular holes at their base that also circumscribe a piezoresistor sensing element. To find the optimum design, the effects of change in cantilever width, rectangular hole length and type of dopant on mechanical properties like deflection, frequency and maximum stress are characterised using finite element analysis software. The surface stress sensitivity characteristics of the different cantilever designs is ascertained by applying a surface stress on their top surfaces. Results show that the sensitivity is increased by increasing the cantilever width as well as the length of the hole and the sensitivity of p-type designs is more than two times the n-type.

Characterization of a gold coated cantilever surface for biosensing applications

Cantilever based sensors are a promising tool for a very diverse spectrum of biological sensors. They have been used for the detection of proteins, DNA, antigens, bacteria viruses and many other biologically relevant targets. Although cantilever sensing has been described for over 20 years, there are still no viable commercial cantilever-based sensing products on the market. Several reasons can be found for this - a lack of detailed understanding of the origin of signals being an important one. As a consequence application-relevant issues such as shelf life and robust protocols distinguishing targets from false responses have received very little attention. Here, we will discuss a cantilever sensing platform combined with an electrochemical system. The detected surface stress signal is modulated by applying a square wave potential to a gold coated cantilever. The square wave potential induces adsorption and desorption onto the gold electrode surface as well as possible structural changes of the target and probe molecules on the cantilever surface resulting in a measurable surface stress change. What sets this approach apart from regular cantilever sensing is that the quantification and identification of observed signals due to target-probe interactions are not only a function of stress value (i.e. amplitude), but also of the temporal evolution of the stress response as a function of the rate and magnitude of the applied potential change, and the limits of the potential change. This paper will discuss three issues that play an important role in future successful applications of cantilever-based sensing. First, we will discuss what is required to achieve a large surface stress signal to improve sensitivity. Second, a mechanism to achieve an optimal probe density is described that improves the signal-to-noise ratio and response times of the sensor. Lastly, lifetime and long term measurements are discussed.

Plasmonic nanobiosensor based on hairpin DNA for detection of trace oligonucleotides biomarker in cancers

MicroRNAs (miRNAs), a class of small, endogenous, noncoding RNA molecules, can serve as biomarkers for potential applications in cancer diagnosis, prognosis, and prediction due to its abnormal expression. As a result, a novel label-free biosensor with nanometer scale was prepared and employed in the detection of trace oligonucleotides based on the localized surface plasmon resonance (LSPR). The dielectric constant on the surface of DNA modified gold nanoparticle would change when probe single-strand DNA hybridized with target oligonucleotides, which resulted in the notable red shift of scattering peak position. The biosensor with excellent selectivity can be used in a real-time monitoring hybridization process. Notably, this method provided label-free detection of DNA and miRNA at single nanoparticle level with limit of detection up to 3 nM. Due to the advantages of LSPR scattering spectra, single nanoparticle biosensor can be designed for trace cancer-relevant miRNAs detection in the future.

Complementary metal oxide semiconductor compatible silicon nanowires-on-a-chip: fabrication and preclinical validation for the detection of a cancer prognostic protein marker in serum

An integrated translational biosensing technology based on arrays of silicon nanowire field-effect transistors (SiNW FETs) is described and has been preclinically validated for the ultrasensitive detection of the cancer biomarker ALCAM in serum. High-quality SiNW arrays have been rationally designed toward their implementation as molecular biosensors. The FET sensing platform has been fabricated using a complementary metal oxide semiconductor (CMOS)-compatible process. Reliable and reproducible electrical performance has been demonstrated via electrical characterization using a custom-designed portable readout device. Using this platform, the cancer prognostic marker ALCAM could be detected in serum with a detection limit of 15.5 pg/mL. Importantly, the detection could be completed in less than 30 min and span a wide dynamic detection range (∼10(5)). The SiNW-on-a-chip biosensing technology paves the way to the translational clinical application of FET in the detection of cancer protein markers.

Design of surface modifications for nanoscale sensor applications

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges.

Detecting nanoscale vibrations as signature of life

The existence of life in extreme conditions, in particular in extraterrestrial environments, is certainly one of the most intriguing scientific questions of our time. In this report, we demonstrate the use of an innovative nanoscale motion sensor in life-searching experiments in Earth-bound and interplanetary missions. This technique exploits the sensitivity of nanomechanical oscillators to transduce the small fluctuations that characterize living systems. The intensity of such movements is an indication of the viability of living specimens and conveys information related to their metabolic activity. Here, we show that the nanomotion detector can assess the viability of a vast range of biological specimens and that it could be the perfect complement to conventional chemical life-detection assays. Indeed, by combining chemical and dynamical measurements, we could achieve an unprecedented depth in the characterization of life in extreme and extraterrestrial environments.

Hybrid spin-microcantilever sensor for environmental, chemical, and biological detection

Nowadays hybrid spin-micro/nanomechanical systems are being actively explored for potential quantum sensing applications. In combination with the pump-probe technique or the spin resonance spectrum, we theoretically propose a realistic, feasible, and an exact way to measure the cantilever frequency in a hybrid spin-micromechanical cantilever system which has a strong coherent coupling of a single nitrogen vacancy center in the single-crystal diamond cantilever with the microcantilever. The probe absorption spectrum which exhibits new features such as mechanically induced three-photon resonance and ac Stark effect is obtained. Simultaneously, we further develop this hybrid spin-micromechanical system to be an ultrasensitive mass sensor, which can be operated at 300 K with a mass responsivity 0.137 Hz ag(-1), for accurate sensing of gaseous or aqueous environments, chemical vapors, and biomolecules. And the best performance on the minimum detectable mass can be [Formula: see text] in vacuum. Finally, we illustrate an in situ measurement to detect Angiopoietin-1, a marker of tumor angiogenesis, accurately with this hybrid microcantilever at room temperature.

Detection of cancer biomarkers in serum using a hybrid mechanical and optoplasmonic nanosensor

Blood contains a range of protein biomarkers that could be used in the early detection of disease. To achieve this, however, requires sensors capable of detecting (with high reproducibility) biomarkers at concentrations one million times lower than the concentration of the other blood proteins. Here, we show that a sandwich assay that combines mechanical and optoplasmonic transduction can detect cancer biomarkers in serum at ultralow concentrations. A biomarker is first recognized by a surface-anchored antibody and then by an antibody in solution that identifies a free region of the captured biomarker. This second antibody is tethered to a gold nanoparticle that acts as a mass and plasmonic label; the two signatures are detected by means of a silicon cantilever that serves as a mechanical resonator for 'weighing' the mass of the captured nanoparticles and as an optical cavity that boosts the plasmonic signal from the nanoparticles. The capabilities of the approach are illustrated with two cancer biomarkers: the carcinoembryonic antigen and the prostate specific antigen, which are currently in clinical use for the diagnosis, monitoring and prognosis of colon and prostate cancer, respectively. A detection limit of 1 × 10(-16) g ml(-1) in serum is achieved with both biomarkers, which is at least seven orders of magnitude lower than that achieved in routine clinical practice. Moreover, the rate of false positives and false negatives at this concentration is extremely low, ∼10(-4).

Diffusion in low-dimensional lipid membranes

The diffusion behavior of biological components in cellular membranes is vital to the function of cells. By collapsing the complexity of planar 2D membranes down to one dimension, fundamental investigations of bimolecular behavior become possible in one dimension. Here we develop lipid nanolithography methods to produce membranes, under fluid, with widths as low as 6 nm but extending to microns in length. We find reduced lipid mobility, as the width is reduced below 50 nm, suggesting different lipid packing in the vicinity of boundaries. The insertion of a membrane protein, M2, into these systems, allowed characterization of protein diffusion using high-speed AFM to demonstrate the first membrane protein 1D random walk. These quasi-1D lipid bilayers are ideal for testing and understanding fundamental concepts about the roles of dimensionality and size on physical properties of membranes from energy transfer to lipid packing.

All-organic microelectromechanical systems integrating specific molecular recognition--a new generation of chemical sensors

Cantilever-type all-organic microelectromechanical systems based on molecularly imprinted polymers for specific analyte recognition are used as chemical sensors. They are produced by a simple spray-coating-shadow-masking process. Analyte binding to the cantilever generates a measurable change in its resonance frequency. This allows label-free detection by direct mass sensing of low-molecular-weight analytes at nanomolar concentrations.

Nanomechanical sensors for single microbial cell growth monitoring

A nanomechanical technique for rapid real time detection and monitoring of microorganism growth will significantly reduce costs and diagnosis times in industrial and clinical settings. Owing to their label free detection mechanism and unprecedented sensitivity to the mass and elastic modulus of biological structures, dynamically operated cantilever arrays provide an opportunity to rapidly detect and track the evolution of microbial growth. Here we report the monitoring of the growth of single Aspergillus niger spores via the multimode response of microcantilevers. The fungal hyphal structure affects the cantilevers' nanomechanical properties as it propagates along the sensor. We demonstrate, for the first time, the mapping of cellular events with great accuracy using a cantilever frequency response. Imaging of growth conditions on the cantilever, which is performed in parallel, allows for verification of these results. Theoretical comparison and finite element modelling confirm experimental findings and allow for determination of the hyphal elastic modulus.

Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides

We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors.