Electrochemical detection of quorum sensing signaling molecules by dual signal confirmation at microelectrode arrays

n-Acyl homoserine lactones (AHLs) are produced by gram-negative bacteria to regulate gene expression in a cell density dependent manner. For instance, expression of virulence factors by pathogens such as Pseudomonas aeruginosa is induced only when a threshold concentration of AHLs is reached, which indicates that the bacterial population is big enough to promote infection. In this study, the indicator strain Agrobacterium tumefaciens NTL4 (pZLR4), which carries a β-galactosidase (β-gal) reporter gene under the control of a quorum sensing promoter, was used to develop an electrochemical biosensor to detect AHLs using the model n-(3-oxo)-dodecanoyl-L-homoserine lactone (oxo-C12-HSL), an AHL previously detected in cystic fibrosis patients infected with P. aeruginosa. The substrate 4-aminophenyl β-D-galactopyranoside was used to detect β-gal activity by cyclic voltammetry. Furthermore, simultaneous monitoring of substrate consumption and p-aminophenol production by β-gal allowed on-chip result verification by dual-signal confirmation. The sensor exhibited high reproducibility and accurately detected oxo-C12-HSL in a low picomolar to low nanomolar range in spiked liquid cultures and artificial saliva, as well as AHLs naturally released by P. aeruginosa in culture supernatants. Moreover, detection took just 2 h, required no sample pretreatment or preconcentration steps, and was easier and faster than traditional methods.     

Surface-enhanced Raman spectroscopy for in situ measurements of signaling molecules (autoinducers) relevant to bacteria quorum sensing

Autoinducer (AI) molecules are used by quorum sensing (QS) bacteria to communicate information about their environment and are critical to their ability to coordinate certain physiological activities. Studying how these organisms react to environmental stresses could provide insight into methods to control these activities. To this end, we are investigating spectroscopic methods of analysis that allow in situ measurements of these AI molecules under different environmental conditions. We found that for one class of AIs, N-acyl-homoserine lactones (AHLs), surface-enhanced Raman spectroscopy (SERS) is a method capable of performing such measurements in situ. SERS spectra of seven different AHLs with acyl chain lengths from 4 to 12 carbons were collected for the first time using Ag colloidal nanoparticles synthesized via both citrate and borohydride reduction methods. Strong SERS spectra were obtained in as little as 10 seconds for 80 microM solutions of AI that exhibited the strongest SERS response, whereas 20 seconds was typical for most AI SERS spectra collected during this study. Although all spectra were similar, significant differences were detected in the SERS spectra of C4-AHL and 3-oxo-C6-AHL and more subtle differences were noted between all AHLs. Initial results indicate a detection limit of approximately 10(-6)M for C6-AHL, which is within the limits of biologically relevant concentrations of AI molecules (nM-microM). Based on these results, the SERS method shows promise for monitoring AI molecule concentrations in situ, within biofilms containing QS bacteria. This new capability offers the possibility to "listen in" on chemical communications between bacteria in their natural environment as that environment is stressed.     

Reusable electrochemical sensing platform for highly sensitive detection of small molecules based on structure-switching signaling aptamers

Aptamers are nucleic acids that have high affinity and selectivity for their target molecules. A target may induce the structure switching from a DNA/DNA duplex to a DNA/target complex. In the present study, a reusable electrochemical sensing platform based on structure-switching signaling aptamers for highly sensitive detection of small molecules is developed using adenosine as a model analyte. A gold electrode is first modified with polytyramine and gold nanoparticles. Then, thiolated capture probe is assembled onto the modified electrode surface via sulfur-gold affinity. Ferrocene (Fc)-labeled aptamer probe, which is designed to hybridize with capture DNA sequence and specifically recognize adenosine, is immobilized on the electrode surface by hybridization reaction. The introduction of adenosine triggers structure switching of the aptamer. As a result, Fc-labeled aptamer probe is forced to dissociate from the sensing interface, resulting in a decrease in redox current. The decrement of peak current is proportional to the amount of adenosine. The present sensing system could provide both a wide linear dynamic range and a low detection limit. In addition, high selectivity, good reproducibility, stability, and reusability are achieved. The recovery test demonstrates the feasibility of the designed sensing system for an adenosine assay.     

Multisegment nanowire sensors for the detection of DNA molecules

We describe a novel application for detecting specific single strand DNA sequences using multisegment nanowires via a straightforward surface functionalization method. Nanowires comprising CdTe-Au-CdTe segments are fabricated using electrochemical deposition, and electrical characterization indicates a p-type behavior for the multisegment nanostructures, in a back-to-back Schottky diode configuration. Such nanostructures modified with thiol-terminated probe DNA fragments could function as high fidelity sensors for biomolecules at very low concentration. The gold segment is utilized for functionalization and binding of single strand DNA (ssDNA) fragments while the CdTe segments at both ends serve to modulate the equilibrium Fermi level of the heterojunction device upon hybridization of the complementary DNA fragments (cDNA) to the ssDNA over the Au segment. Employing such multisegment nanowires could lead to the fabrication more sophisticated and high multispecificity biosensors via selective functionalization of individual segments for biowarfare sensing and medical diagnostics applications.     

Capillary electrophoretic method for the detection of bacterial contamination

There has been growing interest in separations-based techniques for the identification and characterization of microorganisms because of the versatility, selectivity, sensitivity, and short analysis times of these methods. A related area of analysis that is scientifically and commercially important is the determination of the presence or complete absence of microbes (in essence, a test for sample sterility). In such a test, it is not of immediate importance to identify a particular microorganism, but rather, to know with a high degree of certainty whether any organism(s) is (are) present. Current regulations require culture-based tests that can take up to 2 weeks to complete. As a rapid alternative, capillary electrophoresis-based methods are examined. Experimental formats are developed that promote the consolidation of all cell types into a single zone (peak) which is separated from the electroosmotic flow front and any other interfering molecular constituents. This process can be accomplished using a segment of dilute cetyltrimethylammonium bromide, which serves to temporarily reverse the migration direction of the cells, and another segment of solution containing a "blocking agent", which serves to stop the cell migration and focus them into a narrow zone. Relatively wide-bore capillaries can be used to increase sample size. This approach appears to be effective for a broad spectrum of bacteria, and analyses times are less than 10 min.     

Regulating the quorum sensing signalling circuit to control bacterial virulence: in silico analysis

Pathogenic bacteria employ a communication mechanism, known as quorum sensing (QS), to obtain information about their cell density and to synchronise their behaviour. Most bacteria species use QS signalling circuits to optimise the secretion of virulence factors that damage their host. Recently, QS has been recognised as a target for antimicrobial drugs that can control bacterial infections. Here the QS process is modelled as a state transition graph with transitions depending on the diffusion and local concentration of the QS molecules (autoinducers). Based on this model a simulation tool has been developed to simulate the QS process in both open and confined spaces. Using this simulation tool a number of numerical experiments has been carried out with various strategies of QS circuit regulation. The results of these experiments showed that regulation of the QS signalling circuit can lead to significantly reduced bacterial virulence.     

Phase Detection of the Two-Port FPW Sensor for Biosensing

This study reports the phase detection of the two-port flexural plate wave (FPW) sensor for designing and integrating the miniature system and provides a comprehensive methodology for portable using in the biosensor applications of severe acute respiratory syndrome coronavirus (SARS-CoV). The miniature system mainly utilizes the concept of the frequency divider that involves a divider, a time-based oscillator and a gate to reduce the high frequency, and the FPW sensor is fabricated using microelectromechanical systems (MEMS) technologies for producing a potable biosensing detector. The results demonstrate that the insertion loss decreased about -1.15% dB/degC, and the phase delay was about 2.05deg/(1000 cP). The phaseshift resolution was about 10 mV per degree, and the original frequency of 4.2 MHz was divided by 100 to reduce the frequency to 42 kHz. The SARS-CoV could be detected via the S protein binds to the human angiotensin-converting enzyme 2 (hACE2) as a functional receptor, which would cause the phase delay due to the combining of the antibody with the antigen. Therefore, the feasibility studies provide the information that phase detection is an appropriate low-cost technology via frequency divider for fabricating of the miniature biosensors.     

Multiplexed systems for the detection of ionizing radiation

Twelve different versions of integrating encoding (multiplexed) measurement systems for recording the spatial and angular characteristics of ionizing radiation are presented. Spatial, temporal, and binary modulation of the valid signal is performed by the multiplexed measurement system, which thereby suppresses the contribution of noise to the test results and, in a number of cases, makes it possible to obtain tomographic information. Different types of periodioc (0, 1), (– 1, 1), and (– 1, 0, 1) codes and tables, methods of constructing encoders based on these codes and tables, and the basic parameters of the encoders are described.Translated from Izmeritel'naya Tekhnika, No. 11, pp. 49–54, November, 1995.     

Evolvable social agents for bacterial systems modeling

We present two approaches to the individual-based modeling (IbM) of bacterial ecologies and evolution using computational tools. The IbM approach is introduced, and its important complementary role to biosystems modeling is discussed. A fine-grained model of bacterial evolution is then presented that is based on networks of interactivity between computational objects representing genes and proteins. This is followed by a coarser grained agent-based model, which is designed to explore the evolvability of adaptive behavioral strategies in artificial bacteria represented by learning classifier systems. The structure and implementation of the two proposed individual-based bacterial models are discussed, and some results from simulation experiments are presented, illustrating their adaptive properties.     

Chemiluminescence detection systems for the analysis of explosives

The objective of this paper is to provide a comprehensive review of explosive detection by chemiluminescence (CL) through a summary of the relevant literature in the last 5 years and a synopsis of current research topics and developments. The literature reviewed is specially addressed for the detection of a group of high explosives, containing nitrogen compounds. Most explosives compounds contain either nitro or nitrate groups which make possible their detection and quantification using detection systems based on chemiluminescent reactions. Practical considerations and experimental requirements are indicated, and the possibilities and limitations are evaluated.     

用于新型冠状病毒检测的纳米材料及生物传感技术

新型冠状病毒肺炎(Corona Virus Disease 2019, COVID-19)疫情大流行引起全球对此重大突发公共卫生事件的高度关注。新型冠状病毒(SARS-CoV-2)经过多次突变,出现传染速度加快、免疫逃逸、隐匿性传播等特性,令防控形势至今仍异常严峻。对患者的早发现、早隔离仍然是目前最有效的防控措施。因此,迫切需要快速、高灵敏的检测手段来甄别此病毒,以便及早识别感染者。本文简要介绍了SARS-CoV-2的一般特征,并针对核酸、抗体、抗原及病原体作为检测靶标的不同检测手段及最新进展进行分类概述;对一些光学、电学、磁学以及可视化的新型纳米传感器在SARS-CoV-2检测技术上的应用进行了分析。鉴于纳米技术的应用在提高检测灵敏度、特异性以及准确率上具有优势,本文详细介绍了新型纳米传感器在SARS-CoV-2检测中的研究进展,包括表面增强拉曼基生物传感器、电化学生物传感器、磁纳米生物传感器以及比色生物传感器等,并探讨了纳米材料在新型生物传感器构建中的作用和挑战,为纳米材料研究人员开发各种类型的冠状病毒传感技术提供思路。     

Surface-immobilized peptide aptamers as probe molecules for protein detection

We demonstrate the use of surface-immobilized, oriented peptide aptamers for the detection of specific target proteins from complex biological solutions. These peptide aptamers are target-specific peptides expressed within a protein scaffold engineered from the human protease inhibitor stefin A. The scaffold provides stability to the inserted peptides and increases their binding affinity owing to the resulting three-dimensional constraints. A unique cysteine residue was introduced into the protein scaffold to allow orientation-specific surface immobilization of the peptide aptamer and to ensure exposure of the binding site to the target solution. Using dual-polarization interferometry, we demonstrate a strong relationship between binding affinity and aptamer orientation and determine the affinity constant KD for the interaction between an oriented peptide aptamer ST(cys+)_(pep9) and the target protein CDK2. Further, we demonstrate the high selectivity of the peptide aptamer STM_(pep9) by exposing surface-immobilized ST(cys+)_(pep9) to a complex biological solution containing small concentrations of the target protein CDK2.     

Femtosecond resonance enhanced CARS for background-free detection of organic molecules

We study the coherent excitation profile (CEP) of resonance enhanced femtosecond CARS in a model system zinc phthalocyanine in a polymer film host as a prospective technique for detection and identification of molecular species in ambient environments. A new method of suppressing the non-resonant FWM background is demonstrated. Transform theory is applied to calculate CEP based on the absorption spectrum, and good agreement between theory and experiment is obtained.     

Construction of spores for portable bacterial whole-cell biosensing systems

Whole-cell sensing systems based on living genetically engineered bacteria are known to have high sensitivity, selectivity, and rapid response times. Although these systems have found applications in biomedical and environmental analyses, their limited shelf life and transportability still restrict their use for on-site monitoring of analytes. To that end, we have developed a new method for the long-term preservation, storage, and transport of whole-cell biosensing systems that is based on bacterial spores, a dormant form of life. Specifically, we have employed spore-forming bacteria such as Bacillus subtilis and Bacillus megaterium for development of luminescent sensing systems for two model analytes, namely, arsenic and zinc. These sensing cells were converted to spores, which can then be "revived" (germinated) at a later time to generate viable and metabolically active cells. Herein, we demonstrate that these spore-based sensing systems retained their analytical performance, in terms of detection limit, dynamic range, and reproducibility, after storage at room temperature for at least 6 and 8 months, respectively, as well as after three cycles where the cells alternated between being dormant or active, i.e., sporulation-germination cycles. The ability to cycle the sensing cells between active and dormant states prolongs the cell's lifetimes and increases their robustness and ruggedness, thus making them more amenable for field applications. In addition, the small size of spores allows for their easy transport and incorporation in miniaturized portable devices. Finally, we envision that this novel strategy could expand the use of whole-cell biosensors for on-site sensing not only in mild environments but also in harsh environments and locations where there is no easy access to a laboratory, e.g., in developing countries.     

High-throughput microfluidic systems for disease detection

Accuracy and rapid response are critical to the detection of an acute infectious disease, not only because the detection results can affect the medical treatment, but also can prevent disease outbreaks. Since the current culture-based technology is time consuming and experience dependent, academia and industrial researchers are using microfluidics and nucleic acids as the fundamental ideas to build pioneering tools against infectious disease. While many point-of-care microfluidic systems have been realized to execute nucleic acid applications, high-throughput microfluidic systems are under development for various nucleic acid applications because of high efficiency and demand from the market. Building a high-throughput system is an interdisciplinary challenge because of the design concerns from science and the manufacturing concerns from engineering, but its realization will be a milestone. This article is aimed to review three essential steps of the nucleic acid-based detection realized in high-throughput formats, including polymerase chain reaction, capillary electrophoresis, and nucleic acid purification.     

Comparison of glycosphingolipids and antibodies as receptor molecules for ricin detection

Glycosphingolipids (GSLs) have been shown to undergo strong interactions with a number of protein toxins, including potential bioterrorism agents such as ricin and botulinum neurotoxin. Characterization of this interaction in recent years has led to a number of studies where GSLs were used as the recognition molecules for biosensing applications. Here, we offer a comparison of quartz crystal microbalance (QCM) sensors for the detection of ricin using antibodies and the GSLs GM1 and asialoGM1, which have been shown to undergo strong interactions with ricin. The presence, orientation, and activity of the GSL and antibody films were confirmed using ellipsometry, Fourier transform infrared spectroscopy (FT-IR), and QCM. It was found that the GSLs offered more sensitive detection limits when directly compared with antibodies. Both GSLs had lower detection limits at 5 microg/mL, approximately 5 times lower than were found for antibodies (25 microg/mL), and their linear detection range extended to the highest concentrations tested (100 microg/mL), almost an order of magnitude beyond the saturation point for the antibody sensors. Potential sites for nonspecific adsorption were blocked using serum albumin without sacrificing toxin specificity.     

A hybrid plasmonic-photonic nanodevice for label-free detection of a few molecules

Noble metal nanowaveguides supporting plasmon polariton modes are able to localize the optical fields at nanometer level for high sensitivity biochemical sensing devices. Here we report on the design and fabrication of a novel photonic-plasmonic device which demonstrates label-free detection capabilities on single inorganic nanoparticles and on monolayers of organic compounds. In any case, we determine the Raman scattering signal enhancement and the device detection limits that reach a number of molecules between 10 and 250. The device can be straightforwardly integrated in a scanning probe apparatus with the possibility to match topographic and label-free spectroscopic information in a wide range of geometries.