Intact Histological Characterization of Brain-implanted Microdevices and Surrounding Tissue

Research into the design and utilization of brain-implanted microdevices, such as microelectrode arrays, aims to produce clinically relevant devices that interface chronically with surrounding brain tissue. Tissue surrounding these implants is thought to react to the presence of the devices over time, which includes the formation of an insulating "glial scar" around the devices. However, histological analysis of these tissue changes is typically performed after explanting the device, in a process that can disrupt the morphology of the tissue of interest.Here we demonstrate a protocol in which cortical-implanted devices are collected intact in surrounding rodent brain tissue. We describe how, once perfused with fixative, brains are removed and sliced in such a way as to avoid explanting devices. We outline fluorescent antibody labeling and optical clearing methods useful for producing an informative, yet thick tissue section. Finally, we demonstrate the mounting and imaging of these tissue sections in order to investigate the biological interface around brain-implanted devices.     

Whole blood optical biosensor

The future of rapid point-of-care diagnostics depends on the development of cheap, noncomplex, and easily integrated systems to analyze biological samples directly from the patient (e.g. blood, urine, and saliva). A key concern in diagnostic biosensing is signal differentiation between non-specifically bound material and the specific capture of target molecules. This is a particular challenge for optical detection devices in analyzing complex biological samples. Here we demonstrate a porous silicon (PSi) label-free optical biosensor that has intrinsic size-exclusion filtering capabilities which enhances signal differentiation. We present the first demonstration of highly repeatable, specific detection of immunoglobulin G (IgG) in serum and whole blood samples over a typical physiological range using the PSi material as both a biosensor substrate and filter.     

Synthetic circuits,devices and modules

The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.     

Optical-Resolution Photoacoustic Microscopy: Auscultation of Biological Systems at the Cellular Level

Photoacoustic microscopy (PAM) offers unprecedented sensitivity to optical absorption and opens a new window to study biological systems at multiple length- and timescales. In particular, optical-resolution PAM (OR-PAM) has pushed the technical envelope to submicron length scales and millisecond timescales. Here, we review the state of the art of OR-PAM in biophysical research. With properly chosen optical wavelengths, OR-PAM can spectrally differentiate a variety of endogenous and exogenous chromophores, unveiling the anatomical, functional, metabolic, and molecular information of biological systems. Newly uncovered contrast mechanisms of linear dichroism and Förster resonance energy transfer further distinguish OR-PAM. Integrating multiple contrasts and advanced scanning mechanisms has capacitated OR-PAM to comprehensively interrogate biological systems at the cellular level in real time. Two future directions are discussed, where OR-PAM holds the potential to translate basic biophysical research into clinical healthcare.     

Biotechnological synthesis of functional nanomaterials

Biological systems, especially those using microorganisms, have the potential to offer cheap, scalable and highly tunable green synthetic routes for the production of the latest generation of nanomaterials. Recent advances in the biotechnological synthesis of functional nano-scale materials are described. These nanomaterials range from catalysts to novel inorganic antimicrobials, nanomagnets, remediation agents and quantum dots for electronic and optical devices. Where possible, the roles of key biological macromolecules in controlling production of the nanomaterials are highlighted, and also technological limitations that must be addressed for widespread implementation are discussed.     

Micropatterning proteins and synthetic peptides on solid supports: a novel application for microelectronics fabrication technology.

In this paper, we describe a method for immobilizing proteins and synthesizing peptides in micrometer-dimension patterns on solid supports. Microelectronics fabrication technology was adapted and used to lithographically direct the location of immobilization of proteins on appropriately derivatized surfaces. As examples, we micropatterned the protein bovine serum albumin (BSA) and the enzyme horseradish peroxidase (HRP). The catalytic activity of HRP was shown to be retained after being cross-linked to the support. When coupled with solid-phase peptide synthesis, the technique allowed synthetic peptides to be constructed in patterns again having micrometer dimensions. Synthetic polypeptides, polylysine, were constructed in patterns with dimensions that approached the practical limit of resolution for optical lithography at 1-2 microns. The patterns of immobilized molecules and synthetic peptides were visualized using histochemical methods together with light and fluorescence microscopy. The protein and peptide patterning technique described here is an advance in the field of bioelectronics. In particular, it should now be possible to devise novel methods for interfacing with biological systems and constructing new devices for incorporation into miniaturized biosensors.     

便携式生物光学传感器的研究进展

生物光学传感器是一种对生物物质敏感并将其浓度转换为光信号,再由光电器件转换成电信号进行检测的仪器。由于随着微加工技术和纳米技术的进步,生物光学传感器将不断的微型化,各种便携式生物光学传感器的出现使得人们在家中进行疾病诊断、在市场上直接检测食品及在野外快速检测环境污染成为可能。便携式生物光学传感器一般由光源、光学通路和光电元件三部分组成。传感器结构中各个组件的优化处理将有利于检测设备在实际运用中的便利性和在复杂环境中的适用性,同时也有利于提高生物检测的灵敏度。主要从激励光源的选择、生物光学检测的原理、用于传感光源分析的半导体光敏元件3方面,描述近年来常见的便携式生物光学传感器的研究进展。未来生物检测器件将趋于成本低廉、便携快捷、智能高效等特点,基于生物光学反应特性的研究和传感器结构制备的优化将使得便携式生物光学传感器在未来传感检测应用中具有巨大的商业价值和广泛的实用价值。     

Optical immunosensing systems--meeting the market needs

Optical immunosensors and sensing systems are biosensors which produce a quantitative measure of the amount of antibody, antigen or hapten present in a complex sample such as serum or whole blood. The market needs for such devices and their associated instrumentation are reviewed. A brief history of the development of optical immunosensors is presented and the performance of the most well-developed optical immunosensors for meeting these market needs is reviewed. One device, the fluorescent capillary fill device (FCFD) is reviewed in detail with respect to it fulfilling the market needs for an optical immunosensor. Areas for the future development of such sensing systems are also discussed.     

BIOSENSORS: BLESSING OR BANE?

Biosensor technology is changing the methodology used to detect or characterize many microorganisms and/or their metabolites of importance to food microbiologists and the food industry. Biosensors have been developed to monitor the freshness of meat and fish. ATP and glucose concentrations have been monitored as well as continuous control operations in food processing. Enzyme-substrate transformations, DNA or RNA hybridizations and antibody-antigen interactions are examples of the types of molecules used in biosensor systems. Instrumentation coupled to the biological molecules and measuring the changes that occur include reactions on simple ion-sensing electrodes, as well as complex chips, optical fibers or piezoelectric crystals. In most cases, data can be obtained within a few minutes on very small amounts of compounds. However, the long term stability of the biological molecules involved in these procedures presents a major stumbling block. Partially or completely disposable devices are under consideration.     

A starter kit for point-localization super-resolution imaging

Super-resolution fluorescence imaging can be achieved through the localization of single molecules. By using suitable dyes, optical configurations, and software, it is possible to study a wide variety of biological systems. Here, we summarize the different approaches to labeling proteins. We review proven imaging modalities, and the features of freely available software. Finally, we give an overview of some biological applications. We conclude by synthesizing these different technical aspects into recommendations for standards that the field might apply to ensure quality of images and comparability of algorithms and dyes.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

Chemoselective biosensors

New opportunities for biosensors are now appearing in clinical and genetic diagnostics, genomics, environmental protection, food processing and safety, drug discovery and bioprocess monitoring. Concerns about the cost, stability and selectivity of previous sensor technologies are being addressed by developing new recognition systems and their integration into transducers, micro- and nanofabricated devices, array technologies and novel magnetic, acoustic and optical transduction systems.     

合成生物学及其在生物技术中的应用进展

合成生物学是一门21世纪生物学的新兴学科,它着眼生物科学与工程科学的结合,把生物系统当作工程系统"从下往上"进行处理,由"单元"(unit)到"部件"(device)再到"系统"(system)来设计,修改和组装细胞构件及生物系统.合成生物学是分子和细胞生物学、进化系统学、生物化学、信息学、数学、计算机和工程等多学科交叉的产物.目前研究应用包括两个主要方面:一是通过对现有的、天然存在的生物系统进行重新设计和改造,修改已存在的生物系统,使该系统增添新的功能.二是通过设计和构建新的生物零件、组件和系统,创造自然界中尚不存在的人工生命系统.合成生物学作为一门建立在基因组方法之上的学科,主要强调对创造人工生命形态的计算生物学与实验生物学的协同整合.必须强调的是,用来构建生命系统新结构、产生新功能所使用的组件单元既可以是基因、核酸等生物组件,也可以是化学的、机械的和物理的元件.本文跟踪合成生物学研究及应用,对其在DNA水平编程、分子修饰、代谢途径、调控网络和工业生物技术等方面的进展进行综述.     

Biotechnology at low Reynolds numbers.

The shrinking of liquid handling systems to the micron and submicron size range entails moving into the area of small Reynolds numbers. The fluid dynamics in this regime are very different from the macroscale. We present an intuitive explanation of how the different physics of small Reynolds numbers flow, along with microscopic sizes, can influence device design, and give examples from our own work using fluid flow in microfabricated devices designed for biological processing.     

Proteomics: a technology-driven and technology-limited discovery science

An emerging field for the analysis of biological systems is the study of the complete protein complement of the genome, the 'proteome'. There are several complementary tools available for proteome analysis including 2D protein electrophoresis and mass spectrometry. Emerging technologies for proteome analysis include spotted-array-based methods and microfluidic devices. Taken together, these technologies provide a wealth of information that is useful in discovery-based science. However, there are some key limitations of these approaches and new technology is required to be able to fully integrate proteomic information with information obtained about DNA sequence, mRNA profiles and metabolite concentrations into effective models of biological systems.     

Evaluation of a fiberoptic-based system for measurement of optical properties in highly attenuating turbid media

Background  

Accurate measurements of the optical properties of biological tissue in the ultraviolet A and short visible wavelengths are needed to achieve a quantitative understanding of novel optical diagnostic devices. Currently, there is minimal information on optical property measurement approaches that are appropriate for in vivo measurements in highly absorbing and scattering tissues. We describe a novel fiberoptic-based reflectance system for measurement of optical properties in highly attenuating turbid media and provide an extensive in vitro evaluation of its accuracy. The influence of collecting reflectance at the illumination fiber on estimation accuracy is also investigated.     

Protein-polymer nano-machines. Towards synthetic control of biological processes

The exploitation of nature's machinery at length scales below the dimensions of a cell is an exciting challenge for biologists, chemists and physicists, while advances in our understanding of these biological motifs are now providing an opportunity to develop real single molecule devices for technological applications. Single molecule studies are already well advanced and biological molecular motors are being used to guide the design of nano-scale machines. However, controlling the specific functions of these devices in biological systems under changing conditions is difficult. In this review we describe the principles underlying the development of a molecular motor with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for control of the motor function. The molecular motor is a derivative of a TypeI Restriction-Modification (R-M) enzyme and the synthetic polymer is drawn from the class of materials that exhibit a temperature-dependent phase transition.The potential exploitation of single molecules as functional devices has been heralded as the dawn of new era in biotechnology and medicine. It is not surprising, therefore, that the efforts of numerous multidisciplinary teams 12. have been focused in attempts to develop these systems. as machines capable of functioning at the low sub-micron and nanometre length-scales 3. However, one of the obstacles for the practical application of single molecule devices is the lack of functional control methods in biological media, under changing conditions. In this review we describe the conceptual basis for a molecular motor (a derivative of a TypeI Restriction-Modification enzyme) with numerous potential applications in nanotechnology and the use of specific synthetic polymers as prototypic molecular switches for controlling the motor function 4.     

Protein conducting channels-mechanisms, structures and applications

In the past decade among the main developments in the field of bionanotechnology is the application of proteins in devices. Research focuses on the modification of enzyme systems by means of chemical and physical tools in order to achieve full control of their function and to employ them for specific tasks. Membrane protein channels are intriguing biological devices as they allow the recognition and passage of a variety of macromolecules through an otherwise impermeable lipid bilayer. Hence, membrane proteins can be used as sensory devices for detection or as molecular nanovalves to allow for the controlled release of molecules. Here, we discuss the structure and function of three different channel proteins that mediate the membrane passage of macromolecules using different mechanisms. These systems are described in a comparative manner and an overview is provided of the technological advances in employing these proteins in external (or human) controllable devices.     

Foundations for the design and implementation of synthetic genetic circuits

Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes. In other engineering disciplines, a formalized design process has greatly enhanced the scope and rate of success of projects. When engineering biological systems, a desired function must be achieved in a context that is incompletely known, is influenced by stochastic fluctuations and is capable of rich nonlinear interactions with the engineered circuitry. Here, we review progress in the provision and engineering of libraries of parts and devices, their composition into large systems and the emergence of a formal design process for synthetic biology.