生物芯片、生物传感器和生物信息学

近年来,在生物技术和医学研究领域涌现出了许多新技术平台,其中就包括生物芯片技术和生物传感器技术。生物芯片和生物传感器的构建都必须以生物信息学为基础,而两种技术平台应用所得出的数据和结果又反过来大大丰富和充实了生物信息学本身。本分析概述了生物芯片和生物传感器两种技术平台以及生物信息学,对三之间的相互关系进行了讨论。     

Sensitivity Analysis of Gold Nanorod Biosensors for Single Molecule Detection

Single protein molecule detection is important for investigating molecular behavior and diagnosing diseases at an early stage. Gold nanorod (GNR) biosensors have shown promise for label-free detection of single protein molecules. However, for widespread applications of GNR biosensors with high sensitivity, detail studies are needed to understand the effects of the sensing environment and the molecular binding dynamics on the sensitivity. In this work, a comprehensive theoretical analysis with variable substrate, buffer, ligand, and binding position of the target molecules shows that GNR biosensors are highly sensitive for single molecule detection of biological samples including critical pathogens such as cancer marker thyroglobulin and human immunodeficiency virus (HIV) marker glycoprotein. We also propose and show that a GNR biosensor with a dielectric cladding layer on the body increases the sensitivity by orders of magnitude compared to other state-of-the-art biosensors.

     

Biosensor for Rapid and Sensitive Detection of Influenza Virus

Influenza viruses continue to threaten human life, causing considerable damage socially and economically. To reduce influenza-related morbidity and mortality, there is an immediate requirement to develop efficient and effective tools to detect the virus. Several methods are currently employed for diagnosing influenza infections in humans, including viral culture, polymerase chain reaction (PCR), and immunoassay. In addition, biosensors are being developed to improve the limitations of the conventional methods. In this article, we review the current progress in investigative techniques, including the development of biosensors having high sensitivity and selectivity and shorter detection time.     

Controlling Optical Absorption of Graphene in Near-infrared Region by Surface Plasmons

Nowadays, graphene has many applications in optical instruments, biosensors, gas sensors, photovoltaic cells, and so on. In this study, we aimed at investigating the optical properties of graphene under the influence of plasmons created in one-dimensional photonic crystal structure by making use of the absorption spectrum. We put the gold photonic crystal in adjacent to graphene and placed an antireflection layer on top of it. Then, we studied the behavior of graphene absorption peaks in a near-infrared region. By analyzing the graphene behavior in this region, we observed that graphene absorption was increased up to 40% and graphene absorption value in absorption peak, absorption peak wavelength, absorption spectra width, and also its absorption spectra in a wide wavelength range from 1000 to 2500 nm, could be controlled by making use of different factors such as the substance of antireflection layer and photonic crystal geometric dimensions. This structure can make many applications possible for graphene such as using it to build biosensors to identify uric acid and some of the lipids that have specific significances in detecting atherosclerotic lesions as well as diagnosing the states of disease.     

Aluminum Nanohole Arrays Fabricated on Polycarbonate for Compact Disc-Based Label-Free Optical Biosensing

Al nanohole array plasmonic biosensors have been fabricated on polycarbonate (PC) substrates from conventional compact discs (CD). Standard micro and nanofabrication processes have been used and optimized to be PC compatible. The viability of this CD-based plasmonic platform for label-free optical biosensing has been demonstrated through a competitive bioassay for biotin analysis using biotin-functionalized dextran-lipase conjugates immobilized on the transducer surface.     

Progress of new label-free techniques for biosensors: a review

The detection techniques used in biosensors can be broadly classified into label-based and label-free. Label-based detection relies on the specific properties of labels for detecting a particular target. In contrast, label-free detection is suitable for the target molecules that are not labeled or the screening of analytes which are not easy to tag. Also, more types of label-free biosensors have emerged with developments in biotechnology. The latest developed techniques in label-free biosensors, such as field-effect transistors-based biosensors including carbon nanotube field-effect transistor biosensors, graphene field-effect transistor biosensors and silicon nanowire field-effect transistor biosensors, magnetoelastic biosensors, optical-based biosensors, surface stress-based biosensors and other type of biosensors based on the nanotechnology are discussed. The sensing principles, configurations, sensing performance, applications, advantages and restriction of different label-free based biosensors are considered and discussed in this review. Most concepts included in this survey could certainly be applied to the development of this kind of biosensor in the future.     

Immunophenotyping of acute lymphoblastic leukemia using immunohistochemistry in bone marrow biopsy specimens

Flow cytometry is the preferred method of diagnosing and immunophenotyping acute lymphoblastic leukemia (ALL). However, there are situations in which immunohistochemical staining (IH) of bone marrow trephine biopsy specimens can be used to provide immunophenotypic information. To evaluate the use of IH and to confirm its value in diagnosing and typing of ALL, we studied 50 cases of denovo ALL that were previously classified into pre B, T and B by morphologic, cytochemical and FC methods. Paraffin embedded bone marrow trephine biopsies sections were stained using a panel of antibodies,namely, myeloperoxidase (MPO), terminal deoxynucleotidyl transferase (TdT), CD10, CD20, CD79a, CD3. The cases included 37 pre BALL, 10 T ALL and 3 mature BALL. TdT was the most commonly expressed antibody and was positive in 41 of 50 cases of ALL (82%) and in 95% of pre B ALL cases. CD79a and CD10 were positive in 68% and 65% of pre B ALL cases, respectively. CD79a showed similar positivity in B ALL cases (66%). CD 20 was positive in 66% of mature B ALL cases but less positive in pre B ALL (22%). CD3 was positive in 70% of T ALL cases and negative in other ALL subtypes. All of the cases were negative for MPO. Diagnosis and immunophenotyping of acute lymphoblastic leukemia is possible using immunohistochemical staining of bone marrow trephine biopsies.     

Conformational biosensor for diagnosis of prion diseases

A fluorescence technology to monitor the proliferation of amyloidogenic neurological disorders is proposed. A crude brain homogenate (0.01%) from animals infected with a transmissible spongiform encephalopathy is employed as a catalytic medium initiating conformational changes in 520 nM polypeptide biosensors (Tris/trifluoroethanol 50% mixture at pH 7). The fluorescence methods utilize pyrene residues covalently attached to the peptide ends. The coil-to-β-strand transitions in biosensor molecules cause elevation of a distinct fluorescence band of the pyrene aggregates (i.e. excimers). This approach enables the detection of infectious prion proteins at fmol, does not require antibody binding or protease treatment. Technology might be adopted for diagnosing a large variety of conformational disorders as well as for generic high-throughput screening of the amyloidogenic potential in plasma.     

Hodgkin lymphoma: flow me?

Combining fine needle aspirate cytology with flow cytometry immunophenotyping for the rapid diagnosis of lymphoproliferative lesions is commonplace practice in many institutions. Yet, a definitive diagnosis of Hodgkin lymphoma in many cases remains elusive, requiring subsequent tissue biopsy confirmation. In this issue of CytoJournal, Hernandez et al explore the potential role of using the increased CD4/CD8 T-cell ratio in lymph node fine needle aspiration specimens as a specific feature in diagnosing Hodgkin lymphoma. CD4/CD8 T-cell ratio comparisons are made with cytomorphologic diagnoses of reactive, atypical, non-Hodgkin lymphoma, and Hodgkin lymphoma cases.     

The Use of Whole-Cell Biosensors to Detect and Quantify Compounds or Conditions Affecting Biological Systems

A new and promising technique in microbial ecology and environmental biology is the use of whole-cell bacterial biosensors. This minireview describes the use of such biosensors for detection and quantification of various compounds and other conditions affecting bacterial expression of different genes. Three types of biosensors (nonspecific, stress-induced, and specific biosensors) are described including their use in different environments. We present tables of published biosensors, including gene fusions, host organisms, and environments in which they are used. We here describe the use of different reporter genes in the construction of biosensors and discuss their use as tools for monitoring the bioavailability of pollutants and their potential use in studying microbial ecology in general.     

Insight of smart biosensors for COVID-19: A review

The review discusses the diagnostic application of biosensors as point-of-care devices in the COVID-19 pandemic. Biosensors are important analytical tools that can be used for the robust and effective detection of infectious diseases in real-time. In this current scenario, the utilization of smart, efficient biosensors for COVID-19 detection is increasing and we have included a few smart biosensors such as smart and intelligent based biosensors, plasmonic biosensors, field effect transistor (FET) biosensors, smart optical biosensors, surface enhanced Raman scattering (SERS) biosensor, screen printed electrode (SPE)-based biosensor, molecular imprinted polymer (MIP)-based biosensor, MXene-based biosensor and metal–organic frame smart sensor. Their significance as well as the benefits and drawbacks of each kind of smart sensor are mentioned in depth. Furthermore, we have compiled a list of various biosensors which have been developed across the globe for COVID-19 and have shown promise as commercial detection devices. Significant challenges in the development of effective diagnostic methods are discussed and recommendations have been made for better diagnostic outcomes to manage the ongoing pandemic effectively.     

Nanotechnology and biosensors

Nanotechnology is playing an increasingly important role in the development of biosensors. The sensitivity and performance of biosensors is being improved by using nanomaterials for their construction. The use of these nanomaterials has allowed the introduction of many new signal transduction technologies in biosensors. Because of their submicron dimensions, nanosensors, nanoprobes and other nanosystems have allowed simple and rapid analyses in vivo. Portable instruments capable of analyzing multiple components are becoming available. This work reviews the status of the various nanostructure-based biosensors. Use of the self-assembly techniques and nano-electromechanical systems (NEMS) in biosensors is discussed.     

Biological and technical challenges for implementation of yeast-based biosensors

Biosensors are low-cost and low-maintenance alternatives to conventional analytical techniques for biomedical, industrial and environmental applications. Biosensors based on whole microorganisms can be genetically engineered to attain high sensitivity and specificity for the detection of selected analytes. While bacteria-based biosensors have been extensively reported, there is a recent interest in yeast-based biosensors, combining the microbial with the eukaryotic advantages, including possession of specific receptors, stability and high robustness. Here, we describe recently reported yeast-based biosensors highlighting their biological and technical features together with their status of development, that is, laboratory or prototype. Notably, most yeast-based biosensors are still in the early developmental stage, with only a few prototypes tested for real applications. Open challenges, including systematic use of advanced molecular and biotechnological tools, bioprospecting, and implementation of yeast-based biosensors in electrochemical setup, are discussed to find possible solutions for overcoming bottlenecks and promote real-world application of yeast-based biosensors.     

Advances in Cell‐Free Biosensors: Principle,Mechanism, and Applications

Synthetic biology has promoted the development of biosensors as tools for detecting trace substances. In the past, biosensors based on synthetic biology have been designed on living cells, but the development of cell biosensors has been greatly limited by defects such as genetically modified organism problem and the obstruction of cell membrane. However, the advent of cell‐free synthetic biology addresses these limitations. Biosensors based on the cell‐free protein synthesis system have the advantages of higher safety, higher sensitivity, and faster response time over cell biosensors, which make cell‐free biosensors have a broader application prospect. This review summarizes the workflow of various cell‐free biosensors, including the identification of analytes and signal output. The detection range of cell‐free biosensors is greatly enlarged by different recognition mechanisms and output methods. In addition, the review also discusses the applications of cell‐free biosensors in environmental monitoring and health diagnosis, as well as existing deficiencies and aspects that should be improved. In the future, through continuous improvement and optimization, the potential of cell‐free biosensors will be stimulated, and their application fields will be expanded.     

Covalent enzyme immobilization by poly(ethylene glycol) diglycidyl ether (PEGDE) for microelectrode biosensor preparation

Poly(ethylene glycol) diglycidyl ether (PEGDE) is widely used as an additive for cross-linking polymers bearing amine, hydroxyl, or carboxyl groups. However, the idea of using PEGDE alone for immobilizing proteins on biosensors has never been thoroughly explored. We report the successful fabrication of microelectrode biosensors based on glucose oxidase, d-amino acid oxidase, and glutamate oxidase immobilized using PEGDE. We found that biosensors made with PEGDE exhibited high sensitivity and a response time on the order of seconds, which is sufficient for observing biological processes in vivo. The enzymatic activity on these biosensors was highly stable over several months when they were stored at 4 °C, and over at least 3d at 37 °C. Glucose microelectrode biosensors implanted in the central nervous system of anesthetized rats reliably monitored changes in brain glucose levels induced by sequential administration of insulin and glucose. PEGDE provides a simple, low cost, non-toxic alternative for the preparation of in vivo microelectrode biosensors.     

DNA based biosensors

Compared to advances in enzyme sensors, immunosensors, and microbial biosensors, relatively little work exists on DNA based biosensors. Here we review the DNA based biosensors that rely on nucleic acid hybridization. Major types DNA biosensors--electrochemical, optical, acoustic, and piezoelectric--are introduced and compared. The specificity and response characteristics of DNA biosensors are discussed. Overall, a promising future is foreseen for the DNA based sensor technology.     

Development of an optimized backbone of FRET biosensors for kinases and GTPases

Biosensors based on the principle of Förster (or fluorescence) resonance energy transfer (FRET) have shed new light on the spatiotemporal dynamics of signaling molecules. Among them, intramolecular FRET biosensors have been increasingly used due to their high sensitivity and user-friendliness. Time-consuming optimizations by trial and error, however, obstructed the development of intramolecular FRET biosensors. Here we report an optimized backbone for rapid development of highly sensitive intramolecular FRET biosensors. The key concept is to exclude the “orientation-dependent” FRET and to render the biosensors completely “distance-dependent” with a long, flexible linker. We optimized a pair of fluorescent proteins for distance-dependent biosensors, and then developed a long, flexible linker ranging from 116 to 244 amino acids in length, which reduced the basal FRET signal and thereby increased the gain of the FRET biosensors. Computational simulations provided insight into the mechanisms by which this optimized system was the rational strategy for intramolecular FRET biosensors. With this backbone system, we improved previously reported FRET biosensors of PKA, ERK, JNK, EGFR/Abl, Ras, and Rac1. Furthermore, this backbone enabled us to develop novel FRET biosensors for several kinases of RSK, S6K, Akt, and PKC and to perform quantitative evaluation of kinase inhibitors in living cells.     

Making bio-sense of toxicity: new developments in whole-cell biosensors

Bacterial whole-cell biosensors are very useful for toxicity measurements of various samples. Semi-specific biosensors, containing fusions of stress-regulated promoters and reporter genes, have several advantages over the traditional, general biosensors that are based on constitutively expressed reporter genes. Furthermore, semi-specific biosensors are constantly being refined to lower their sensitivity and, in combination, are able to detect a wide range of toxic agents. However, the requirement for a positive response of these biosensors to toxicants can result in false-negative responses. The application of in situ inoculation and single-cell detection, combined with the introduction of new reporter genes and refined detection equipment, could lead to the extensive use of semi-specific, stress-responsive biosensors for toxicity estimations in the future.     

The carbon paste electrode encrusted with a microreactor as glucose biosensor.

The amperometric biosensors based on carbon paste electrodes (CPEs) encrusted with single microreactor (MR) have been constructed for the determination of glucose. The MRs were prepared from CPC-silica carrier (CPC) and were loaded with glucose oxidase (GO), mediator (M) and acceptor (A). As the mediator cation radical of 5,10-dimethyl-5, 10-dihydrophenazine (DMDHP), N-methylphenazonium methyl sulfate (PMS) and o-benzoquinone (BQ) and as the acceptor Fe[EDTA]- or Fe(CN)6(3-) was used. The biosensors acted at electrode potential 0.15-0.27 V versus Ag-AgCl electrode. The calibration graphs of the biosensors were linear in the range from 1.5 to 50 mM of glucose. The sensitivity of the biosensors did not change at pH 6-8. The dissolved oxygen little (7%) influenced the biosensors response and 1 mM of ascorbic acid produced the response that was of equal value to 0.5 mM of glucose. The biosensors showed high stability; no change of the response of the biosensors prepared by using the novel microreactor was observed at least for 6 months by keeping the loaded CPC at room temperature in silica container. An optimization of the biosensors response against the GO, the mediator and the polymer amount was performed. The digital modeling of the biosensors action is following.     

Biosensors based on electrochemical lactate detection: A comprehensive review

Lactate detection plays a significant role in healthcare, food industries and is specially necessitated in conditions like hemorrhage, respiratory failure, hepatic disease, sepsis and tissue hypoxia. Conventional methods for lactate determination are not accurate and fast so this accelerated the need of sensitive biosensors for high-throughput screening of lactate in different samples. This review focuses on applications and developments of various electrochemical biosensors based on lactate detection as lactate being essential metabolite in anaerobic metabolic pathway. A comparative study to summarize the L-lactate biosensors on the basis of different analytical properties in terms of fabrication, sensitivity, detection limit, linearity, response time and storage stability has been done. It also addresses the merits and demerits of current enzyme based lactate biosensors. Lactate biosensors are of two main types – lactate oxidase (LOD) and lactate dehydrogenase (LDH) based. Different supports tried for manufacturing lactate biosensors include membranes, polymeric matrices-conducting or non-conducting, transparent gel matrix, hydrogel supports, screen printed electrodes and nanoparticles. All the examples in these support categories have been aptly discussed. Finally this review encompasses the conclusion and future emerging prospects of lactate sensors.