Methods in Molecular Biology 1572 Ben Prickril Avraham Rasooly Editors Biosensors and Biodetection Methods and Protocols Volume 2: Electrochemical, Bioelectronic, Piezoelectric, Cellular and Molecular Biosensors Second Edition METHODS IN MOLECULAR BIOLOGY Series Editor John M Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Biosensors and Biodetection Methods and Protocols, Volume 2: Electrochemical, Bioelectronic, Piezoelectric, Cellular and Molecular Biosensors Second Edition Edited by Ben Prickril National Cancer Institute National Institutes of Health Rockville, MD, USA Avraham Rasooly National Cancer Institute National Institutes of Health Rockville, MD, USA Editors Ben Prickril National Cancer Institute National Institutes of Health Rockville, MD, USA Avraham Rasooly National Cancer Institute National Institutes of Health Rockville, MD, USA ISSN 1064-3745 ISSN 1940-6029 (electronic) Methods in Molecular Biology ISBN 978-1-4939-6910-4 ISBN 978-1-4939-6911-1 (eBook) DOI 10.1007/978-1-4939-6911-1 Library of Congress Control Number: 2017932742 © Springer Science+Business Media LLC 2009, 2017 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A This book is dedicated to the memory of Adolph and Louise Prickril Preface Biosensor Technologies A biosensor is defined by the International Union of Pure and Applied Chemistry (IUPAC) as “a device that uses specific biochemical reactions mediated by isolated enzymes, immunosystems, tissues, organelles or whole cells to detect chemical compounds usually by electrical, thermal or optical signals” [1]; all biosensors are based on a two-component system: Biological recognition element (ligand) that facilitates specific binding or biochemical reaction with the target analyte Signal conversion unit (transducer) Since the publication of the first edition of this book in 2009, “classical” biosensor modalities such as electrochemical or surface plasmon resonance (SPR) continue to be developed New biosensing technologies and modalities have also been developed, including the use of nanomaterials for biosensors, fiber-optic-based biosensors, genetic code-based sensors, and field-effect transistors and the use of mobile communication device-based biosensors Although it is impossible to describe the fast-moving field of biosensing in a single publication, this book presents descriptions of methods and uses for some of the basic types of biosensors while also providing the reader a sense of the enormous importance and potential for these devices In order to present a more comprehensive overview, the book also describes other biodetection technologies Dr Leland C Clark, who worked on biosensors in the early 1960s, provided an early reference to the concept of a biosensor by developing an “enzyme electrode” for glucose concentration measurement using the enzyme glucose oxidase (GOD) [2] Glucose monitoring is essential for diabetes patients, and even today, the most common clinical biosensor technology for glucose analysis is the electrochemical detection method envisioned by Clark more than 50 years ago Today glucose monitoring is performed using rapid point of care biosensors made possible through advances in electronics that have enabled sensor miniaturization The newest generation of biosensors includes phone-based optical detectors with high-throughput capabilities The Use of Biosensors Biosensors have several potential advantages over other methods of biodetection, including increased assay speed and flexibility Rapid, real-time analysis can provide immediate interactive information to health-care providers that can be incorporated into the planning of patient care In addition, biosensors allow multi-target analyses, automation, and reduced testing costs Biosensor-based diagnostics may also facilitate screening for cancer and other diseases by improving early detection and therefore improving prognosis Such technology may be extremely useful for enhancing health-care delivery to underserved populations and in community settings vii viii Preface The main advantages of biosensors include: Rapid or real-time analysis: Direct biosensors such as those employing surface plasmon resonance (SPR) enable rapid or real-time label-free detection and provide almost immediate interactive sample information This enables facilities to take corrective measures before a product is further processed or released for consumption Point of care detection capabilities: Biosensors can be used for point of care testing This enables state-of-the-art molecular analysis without requiring a laboratory Continuous flow analysis: Many biosensors are designed to allow analysis of bulk liquids In such biosensors, the target analyte is injected onto the sensor using a continuous flow system immobilized in a flow cell or column, thereby enhancing the efficiency of analyte binding to the sensor and enabling continuous monitoring Miniaturization: Increasingly, biosensors are being miniaturized for incorporation into equipment for a wide variety of applications including clinical care, food and dairy analyses, agricultural and environmental monitoring, and in vivo detection of a variety of diseases and conditions Control and automation: Biosensors can be integrated into online process monitoring schemes to provide real-time information about multiple parameters at each production step or at multiple time points during a process, enabling better control and automation of biochemical facilities Biosensor Classification In general, biosensors can be divided into two groups: direct recognition sensors in which the biological interaction is directly measured and indirect detection sensors which rely on secondary elements (often catalytic) such as enzymes or fluorescent tags for measurements Figure illustrates the two types of biosensors In each group, there are several types of A B Recognition Element Recognition Element Transducer Output Interface Fig General schematic of biosensors (A) Direct detection biosensors where the recognition element is label-free and (B) indirect detection biosensors using “sandwich” assay where the analyte is detected by labeled molecule Direct detection biosensors are simpler and faster but typically yield a higher limit of detection compared to indirect detection systems Preface ix optical, electrochemical, or mechanical transducers Although the most commonly used ligands are antibodies, other ligands are being developed including aptamers (proteinbinding nucleic acids) and peptides There are numerous types of direct and indirect recognition biosensors, and the choice of a suitable detector is complex and based on many factors These include the nature of the application, type of labeled molecule (if used), sensitivity required, number of channels (or area) measured, cost, technical expertise, and speed of detection In this book, we describe many of these detectors, their application to biosensing, and their fabrication The transducer element of biosensors converts the biochemical interactions of the ligand into a measurable electronic signal The most important types of transducer used today are optical, electrochemical, and mechanical Direct Label-Free Detection Biosensors Direct recognition sensors, in which the biological interaction is directly measured in real time, typically use non-catalytic ligands such as cell receptors or antibodies Such detectors typically measure directly physical changes (e.g., changes in optical, mechanical, or electrical properties) induced by the biological interaction and not require additional labeled molecules (i.e., are label-free) for detection The most common direct detection biosensors are optical biosensors including biosensors which employ evanescent waves generated when a beam of light is incident on a surface at an angle yielding total reflection Common evanescent wave biosensors are surface plasmon resonance (SPR) or resonant mirror sensors Other direct optical detectors include interferometric sensors or grating coupler Nonoptical direct detection sensors are quartz resonator transducers that measure change in resonant frequency of an oscillating piezoelectric crystal as a function of the mass (e.g., analyte binding) on the crystal surface, microcantilevers used in microelectromechanical systems (MEMS) measuring bending induced by the biomolecular interactions, or field-effect transistor (FET) biosensors, a transistor gated by biological molecules When biological molecules bind to the FET gate, they can change the gate charge distribution resulting in a change in the conductance of the FET Indirect Label-Based Detection Biosensors Indirect detection sensors rely on secondary elements for detection and utilize labeling or catalytic elements such as enzymes Examples of such secondary elements are the enzyme alkaline phosphatase and fluorescently tagged antibodies that enhance detection of a sandwich complex Unlike direct sensors, which directly measure changes induced by biological interaction and are “label-free,” indirect sensors require a labeled molecule bound to the target Most optical indirect sensors are designed to measure fluorescence; however, such sensors can also measure densitometric and colorimetric changes as well as chemiluminescence, depending on the type of label used Electrochemical transducers measure the oxidation or reduction of an electroactive compound on the secondary ligand and are one common type of indirect detection sensor Several types of electrochemical biosensors have been developed including amperometric devices, which detect ions in a solution based on electric current or changes in electric current when an analyte is oxidized or reduced Another common indirect detection biosensor employs optical fluorescence, detecting fluorescence of the secondary ligand via CCD, PMT, photodiode, and spectrofluorometric analysis In addition, visual measurement such as change of color or appearance of bands (e.g., lateral flow detection) can be used for indirect detection x Preface Indirect detection can be combined with direct detection to increase sensitivity or to validate results; for example, the use of secondary antibody in combination with an SPR immunosensor Using a sandwich assay, the analyte captured by the primary antibody is immobilized on the SPR sensor and generates a signal which can be amplified by the binding of a secondary antibody to the captured analyte Ligands for Biosensors Ligands are molecules that bind specifically with the target molecule to be detected The most important properties of ligands are affinity and specificity Of the various types of ligands used in biosensors, immunosensors—particularly antibodies—are the most common biosensor recognition element Antibodies (Abs) are highly specific and versatile and bind strongly and stably to specific antigens However, Ab ligands have limited long-term stability and are difficult to produce in large quantities for multi-target biosensor applications where many ligands are needed Other types of ligands such as aptamers and peptides are more suited to highthroughput screening and chemical synthesis Aptamers are protein-binding nucleic acids (DNA or RNA molecules) selected from random pools based on their ability to bind other molecules with high affinity Peptides are another potentially important class of ligand suitable for high-throughput screening due to their ease of selection However, the affinity of peptides is often lower than that of antibodies or aptamers, and peptides vary widely in structural stability and thermal sensitivity New Trends in Biosensing While the fundamental principles and the basic configuration of biosensors have not changed in the last decade, this book expands the application of these principles using new technologies such as nanotechnology, integrated optics (IO) bioelectronics, portable imaging, new fluidics and fabrication methodologies, and new cellular and molecular approaches Integration of nanotechnology: There has been great progress in nanotechnology and nanomaterial in recent years New nanoparticles have been developed having unique electric conductivity and optical and surface properties For example, in several chapters, new optical biosensors are described that integrate nanomaterials in SPR biosensor configurations such as localized surface plasmon resonance (LSPR), 3D SPR plasmonic nanogap arrays, or gold nanoparticle SPR plasmonic peak shift In addition to SPR biosensors, nanomaterials are also applied to fluorescence detection utilizing fluorescence quantum dot or silica nanoparticles to increase uniform distribution of enzyme and color intensity in colorimetric biosensors or to improve lateral flow detection In addition to optical sensors, gold nanoparticles (AuNPs) have been integrated into electrochemical biosensors to improve electrochemical performance, and magnetic nanoparticles (mNPs) have been used to improve sample preparation Nanoparticlemodified gate electrodes have been used in the fabrication of organic electrochemical transistors Bioelectronics: Several chapters described the integration of biological elements in electronic technology including the use of semiconductors in several configurations of field-effect transistors and light-addressable potentiometric sensors Preface xi Application of imaging technologies: The proliferation of high-resolution imaging technologies has enabled better 2D image analysis and increases in the number of analytical channels available for various modalities of optical detection These include twodimensional surface plasmon resonance imaging (2D-SPRi) utilizing CCD cameras or 2D photodiode arrays The use of smartphones for both fluorescence and colorimetric detectors is described in several manuscripts Integrated optics (IO): Devices with photonic integrated circuits are presented which integrate several optical and often electronic components Examples include an integrated optical (IO) nano-immunosensor based on a bimodal waveguide (BiMW) interferometric transducer integrated into a complete lab-on-a-chip (LOC) platform New fluidics and fabrication methodologies: Fluidics and fluid delivery are important components of many biosensors In addition to traditional polymer-fabricated microfluidics systems, inkjet-printed paper fluidics are described that may play an important role in LOCs and medical diagnostics Such technologies enable low-cost mass production of LOCs In addition, several chapters describe the use of screen printing for device fabrication Cellular and molecular approaches: Molecular approaches are described for aptamer-based biosensors (aptasensors), synthetic cell-based sensors, loop-mediated DNA amplification, and circular strand displacement for point mutation analysis While “classic” transducer modalities such as SPR, electrochemical, or piezoelectric remain the predominant biosensor platforms, new technologies such as nanotechnology, integrated optics, or advanced fluidics are providing new capabilities and improved sensitivity Aims and Approaches This book attempts to describe the basic types, designs, and applications of biosensors and other biodetectors from an experimental point of view We have assembled manuscripts representing the major technologies in the field and have included enough technical information so that the reader can both understand the technology and carry out the experiments described The target audience for this book includes engineering, chemistry, biomedical, and physics researchers who are developing biosensing technologies Other target groups are biologists and clinicians who ultimately benefit from development and application of the technologies In addition to research scientists, the book may also be useful as a teaching tool for bioengineering, biomedical engineering, and biology faculty and students To better represent the field, most topics are described in more than one chapter The purpose of this redundancy is to bring several experimental approaches to each topic, to enable the reader to choose an appropriate design, to combine elements from different designs in order to better standardize methodologies, and to provide readers more detailed protocols Organization The publication is divided into two volumes Volume I (Springer Vol XXX) focuses on optical-based detectors, while Volume II (Springer Vol XXX) focuses on electrochemical, bioelectronic, piezoelectric, cellular, and molecular biosensors Small Bowel Microultrasound a 45 5.5 40 Depth (mm) 35 6.5 30 25 7.5 20 15 8.5 10 9.5 10 11 12 45 5.5 40 Depth (mm) Fiducial marker Length (mm) b 547 35 6.5 30 25 7.5 20 15 8.5 10 9.5 10 11 12 Length (mm) Fig Sequential B-scan reconstructed 2D images of the same porcine small bowel tissue scanned across its short axis using middle speed mode on the μUS continuous sweep scanner and the 48 MHz transducer (a) Without any perfusion (b) Perfusion with 60.0 ml degassed phosphate buffer saline solution shows greater mucosal characterization as illustrated by increased depth of tissue observed 2.2 μUS Step Scanner System Frame to house scanning system (custom built using aluminum pillars fitted onto optical breadboards; Thorlabs Ltd., Ely, UK) Remote Pulser (JSR Ultrasonics, Imaginant Inc., New York, USA) MDO3014 Mixed Domain Oscilloscope (Tektronix UK Ltd., Berkshire, UK) DPR500 Dual Pulser/Receiver (JSR Ultrasonics, Imaginant Inc., New York, USA) SHOT-602, Two-axis Stage Controller (Sigma Koki Co., Ltd., Tokyo, Japan) 548 a Thineskrishna Anbarasan et al 40 Depth (mm) 4.5 35 5.5 30 25 6.5 20 15 7.5 10 8.5 0 10 Length (mm) 12 14 Fiducial marker 40 Depth (mm) 4.5 35 5.5 30 25 6.5 20 15 7.5 10 8.5 0 10 12 14 Length (mm) Fig B-scan reconstructed 2D images of the same porcine small bowel tissue scanned across its short axis using the mid speed mode and the 48 MHz transducer (a) Perfusion with dPBS (b) Perfusion with 60.0 ml dPBS solution and 10 ml M™ Glass bubble mixture 5-phase Stepper Motor (XY axis) (Sigma Koki Co., Ltd., Tokyo, Japan) Laboratory use Mini Scissor Lift Table Computer Terminal 2.3 μUS Continuous Sweep Scanner System Frame to house scanning system (custom built using aluminum pillars fitted onto optical breadboards; Thorlabs Ltd., Ely, UK) Remote Pulser (JSR Ultrasonics, Imaginant Inc., New York, USA) 12-Bit FlexRIO oscilloscope adapter module (NIPX1e-1071, National Instruments, Texas, USA) paired with fieldprogrammable gate array (FPGA) DPR500 Dual Pulser/Receiver (JSR Ultrasonics, Imaginant Inc., New York, USA) Small Bowel Microultrasound 549 Fig (a) Scanning tray prepared with porcine small bowel tissue sample for μUS scan depicting its constituent layers (b) Schematic representation of the cross-section of scanning tray prepared for μUS scan of porcine small bowel tissue Fig (m) Mucosa, (sm) Submucosa, (me) Muscularis propria, (s) Serosa (a) Schematic of porcine small bowel tissue transected on its longitudinal axis and prepared for scan with Polybead® Microspheres 90.0 μm injected in its distal end to serve as μUS fiducial markers (b) B-scan reconstructed 2D image of perfused section of porcine small bowel tissue injected with fiducial markers corresponding to Fig a scanned across its short axis using the μUS step scanner and the 48 MHz transducer Operational amplifier with a gain G ¼ to amplify 12-Bit FlexRIO oscilloscope adapter module signal for DPR500 Dual Pulser/Receiver Two-axis Motion Control and Positioning System (Galil DMC 4132, MotionLink Ltd., Berkshire, UK) Maxon brushless Servo Motors (XY axis) (ML series 3000, MotionLink Ltd Berkshire, UK) with Position Encoders (HEDS 500ppr, MotionLink, Ltd., Berkshire, UK) Laboratory use Mini Scissor Lift Table Computer Terminal 550 Thineskrishna Anbarasan et al 2.4 Ex Vivo Porcine Small Bowel Tissue Phantom Vacuum-sealed abattoir-frozen porcine small bowel tissue sample (Length % 20.0 cm; Medical meat supplies, Oldham, UK) Tissue samples are stored in the freezer Surgical instruments (Iris scissors, Mayo scissors and thumb dressing forceps, arterial forceps) are used for the preparation and transection of the porcine small bowel tissue sample BD ml Luer-Lok™ syringe (Becton, Dickson and Company, New Jersey, USA) Omnifix®-F Solo ml syringe (Braun, Melsungen, Germany) Butterfly™ Winged infusion set 23 G Â ¾00 (Becton, Dickson and Company, New Jersey, USA) Microlance™ Orange 25 G 5/800 (Becton, Dickson and Company, New Jersey, USA) Microlance™ Green 21G 1.500 (Becton, Dickson and Company, New Jersey, USA) Magnifying lamp to aid in preparation of the porcine small bowel tissue sample (Premier Farnell plc, Leeds, UK) Plastipak 60 ml syringe (Becton, Dickson and Company, New Jersey, USA) Perfusor® fm (Braun, Melsungen, Germany) 2.5 Scanning Tray A transparent container is used to hold the acoustic absorber sheet and agar on which the tissue sample is placed for scanning Acoustic absorber sheet 1% (w/w) agar granular powder, General Purpose Grade (Fisher Scientific UK Ltd., Loughborough, UK) 2.6 Working Solutions Degassed phosphate buffered saline (dPBS) (DNase, RNase and protease free filtered through a 0.2 μm filter; pH: 7.4 Æ 0.1; Fisher Scientific UK Ltd., Loughborough, UK) Red Food Coloring (Tesco, UK) Polybead® Microspheres 90.0 μm (Polysciences, Inc., Pennsylvania, USA) M™ Glass microbubbles K1 series (3 M Company, Minnesota, UK) Epidural filters, disc and flat, with Luer Lock connection (PORTEX®, Smiths Medical, Kent, UK) Small Bowel Microultrasound 551 Methods 3.1 μUS Step Scanner System 3.1.1 μUS Step Scanner System Setup 3.1.2 Preparation of μUS Step Scanner System The setup of the μUS slow scanner system comprises two sections: (1) assembly of the frame consisting of the 5-phase step motor (XY axis, Sigma Koki Co., Ltd., Tokyo, Japan) and remote pulser (JSR Ultrasonics, Imaginant Inc., New York, USA); (2) setup of external instrument to coordinate and support the μUS step scanner system as illustrated in the schematic diagram in Fig The frame of the scanning system consists of four aluminum pillars mounted between two optical breadboards (Thorlabs Ltd., Ely, UK) to provide stability during scanning Within the frame, attached to the optical breadboard, the mobile parts of the scanning system are assembled Two-dimensional motion is achieved through the stage motors, depicted by (H) and (I) in Fig The remote pulser has been mounted to these via an L-bracket, with a goniometer for accurate positioning of the transducer to prevent oblique incidence The stage motors are connected to a SHOT—602 twoaxis stage controller (Sigma Koki Co., Ltd., Tokyo, Japan) The MDO3014 mixed domain oscilloscope (Tektronix UK Ltd., Berkshire, UK) records the raw electrical echo signal from the μUS transducer which is then input into a LabVIEW (National Instruments, Texas, USA) program in the computer terminal, custom made to automate the scanning process (see Notes and 2) (a) After the region of interest of the tissue sample to be scanned is decided, it is placed in a scanning tray on a laboratory scissor lift which is subsequently raised to a sufficient height under the remote pulser (b) The transducer is fitted onto the remote pulser and, using the Z-axis controller located on the pulser housing, it is gently lowered into the scanning tray over the tissue region to be scanned The transducer’s focal distance has to be considered in the setup of the tissue sample The depth of focus of the AFMTH19 48 MHz μUS transducer is mm (see Note 3) (c) In the JSR control panel software used to control the DPR500 Dual Pulser/Receiver (JSR Ultrasonics, Imaginant Inc., New York, USA), the following settings are fixed for all scans— Trigger: internal; Pulse energy: 12.4 μJ; Pulse repetition frequency: 200 Hz; Voltage: 143 V; Damping: 100 Ω; Receiver Bandwidth: 5–300 MHz The receiver gain is set at 40 dB prior to initial μUS test scans to determine background noise levels before adjustment as required (d) The DPR500 Dual Pulser/Receiver is switched to pulse mode The scanning tray is subsequently gently shifted such that the μUS transducer is over a region without the tissue to note the receive signal, indicating the presence of the agar and 552 Thineskrishna Anbarasan et al Fig (a) Signals observed on MDO3014 oscilloscope when transducer is positioned above a region of the scanning tray with a layer of agar and acoustic absorber sheet (b) Signals observed on MDO3014 Mixed domain oscilloscope when transducer is positioned above a region of the scanning tray over porcine small bowel tissue pinned to a layer of agar The end of the transducer signal or the time from which the peak amplitude data is acquired is indicated with the cursor (c) Screenshot of custom made LABVIEW program, depicting scan parameters, developed to automate μUS scanning acoustic absorber plate, on the MDO3014 mixed domain oscilloscope as illustrated in Fig 8a The scanning tray is then shifted to the position with the μUS transducer at the origin of the region to be scanned (see Note 4) (e) The acquisition start point noted on the MDO3014 mixed domain oscilloscope as illustrated in Fig 8b, along with scanning parameters including distance and signal averaging, are input into the bespoke LabVIEW program to initiate scanning (see Note 5) 3.1.3 Scanning Algorithm for μUS Step Scanner System On initiation of the μUS scan, scan data is acquired at each step, along the x-direction of the region of interest being scanned The physical distance between these acquisitions is determined by the x step size in the software interface After completing a full pass in the x-direction, the system translates a single step in the y-direction and repeats the process until the end of the configured scanning limits have been reached The algorithm which outlines the automation of the μUS step scanner is illustrated in Fig 9a Small Bowel Microultrasound 553 Fig Scanning automation algorithm for a μUS step scanner b μUS continuous sweep scanner 3.2 μUS Continuous Sweep Scanner System 3.2.1 Setup of μUS Continuous Sweep Scanner System The setup of the μUS continuous sweep scanner system comprises two sections similar to those for the μUS stepping scanner system as described in Subheading 3.1 The frame used in the μUS continuous sweep scanner system is identical to that used in the μUS stepping scanner system Within this frame, the setup of the mobile parts is that used in the μUS step scanner, as described in Subheading 3.1, with the exception of the stage motors Two Maxon 554 Thineskrishna Anbarasan et al brushless servo motors (XY axis) (ML series 3000, MotionLink Ltd Berkshire, UK) are housed to serve as the stage motors These motors have position encoders (HEDS 500ppr, MotionLink, Ltd., Berkshire, UK) which allow the positions of the motors to be accurately measured whilst pulsing This allows scanning of the tissue samples in a continuous fashion unlike in the stepping scanner system The schematic in Fig illustrates the setup of the external system to coordinate and support the μUS continuous sweep scanner system The motor moves continuously at a speed sufficient for averaging of the amplitude scan of a particular location on the tissue sample, with subsequent transferred to storage in the computer terminal for processing 3.2.2 Setup of μUS Continuous Sweep Scanner System (a) The positioning of the tissue sample for μUS continuous sweep scanning is described in Subheading 3.1.2 for the μUS step scanner (b) The DPR500 Dual Pulser/Receiver is then switched on with the μUS transducer positioned over the start point of the region of interest In the JSR control panel software the following settings were fixed as such for all our scans; Trigger: external; Damping: 100 Ω; Pulse energy: 12.40 μJ; Receiver Bandwidth: 5–300 MHz (see Notes and 4) (c) A bespoke LabVIEW program with simultaneous B-scan display is run to determine if the μUS penetration is satisfactory or if the scan settings need adjustment This is because the continuous sweep scanner does not include a separate digital oscilloscope like the μUS stepping scanner To minimize the computer terminal’s memory usage an alternate custom made LabVIEW program without the simultaneous B-scan display is used with the finalized settings to complete the μUS continuous sweep scan (see Notes and 2) 3.2.3 Scanning Algorithm for μUS Continuous Sweep Scanner System The μUS continuous sweep scanner employs a continuous motion of the stage motors in the x-direction, with data acquisitions occurring as quickly as possible until the configured x-limit is reached The B-scan data and x-positions of each data line are then saved to the hard drive If the y-direction parameters have not been satisfied, the motors translate one step in the y-direction and repeat the process The full algorithm for the automation of the μUS continuous sweep scanner is illustrated in Fig 9b 3.3 Porcine Small Bowel Tissue Phantom (a) Fresh frozen porcine small bowel tissue (Medical Meat Supplies, Oldham, UK), obtained vacuum packed, is thawed under a running tap water bath for 15 minutes prior to use The tissue is gently washed on both its external and internal surfaces by running tap water over it and through its lumen The tissue is then placed on a working surface under a 3.3.1 Preparation of Porcine Small Bowel Tissue Small Bowel Microultrasound 555 Fig 10 (a) Thawed porcine small bowel tissue pinned to a working surface (b) Porcine small bowel tissue with superficial mesentery layer flipped over and majority of deep mesentery layer extracted to reveal mesenteric vasculature lying between these layers magnifying lamp (Premier Farnell plc, Leeds, UK) to be prepared for scanning (b) The top layer of the mesentery of the small bowel is decorticated to reveal the mesenteric vasculature lying on the bottom layer of the mesentery (see Note 6) (c) The tissue sample is pinned onto the acoustic absorber sheet using the Microlance™ Orange 25G 5/800 (Becton, Dickson and Company, New Jersey, USA) to allow sufficient exposure of the vasculature for cannulation as illustrated in Fig 10 (d) A Butterfly™ winged infusion set 23 G Â ¾00 (Becton, Dickson and Company, New Jersey, USA) is connected to a BD ml Luer-Lok ™ syringe (Becton, Dickson and Company, 556 Thineskrishna Anbarasan et al Fig 11 (a) Cannulated porcine small bowel perfused with red food coloring solution using a BD ml Luer-Lok ™ syringe (b) Perfused porcine small bowel tissue focused on the small bowel vasculature Comparison with Fig 10a illustrates the difference between pre- and post-perfusion of the tissue with red food coloring solution New Jersey, USA) filled with diluted red food coloring (Tesco, UK) Angled at approximately 15 to the surface of the acoustic absorber sheet, the Butterfly™ winged infusion set needle is gently inserted into a vessel to cannulate it Figure 11 illustrates a successfully cannulated tissue sample (see Notes and 8) (e) To determine if the cannulation is successful the BD ml Luer-Lok™ syringe containing the red dye solution is gently pressed and the mesenteric vasculature of the small bowel tissue sample is observed (see Notes 9, 10 and 11) (f) 60 ml dPBS solution (Fisher Scientific UK Ltd., Loughborough, UK) filled in a Plastipak 60 ml syringe (Becton, Dickson and Company, New Jersey, USA) is perfused into the cannulated mesenteric vessel of the tissue sample using a Perfusor® fm (Braun, Melsungen, Germany) at a rate of 200 ml/h Small Bowel Microultrasound 557 Fig 12 Schematic of the cross section of porcine small bowel tissue (a) Shows bifurcation of mesenteric vessel to supply the superficial and deep surfaces of a cannulated small bowel (b) Shows the axis of transection (dashed line) on the surface of the cannulated small bowel adjacent to the superficial edge of the mesentery After incision, the superficial layer of the small bowel tissue is flipped over as indicated by the arrow to expose the internal surface for μUS scan (c) Shows porcine small bowel tissue prepared for μUS scan with the internal surface exposed for scanning (g) Post-perfusion, the cannula is removed from the tissue and the small bowel tissue is transected adjacent to the upper edge of the mesentery as illustrated in Fig 12 and flipped over to expose the lumen for scanning (h) The tissue is trimmed and the region of interest for scanning is to be pinned using Microlance™ Orange 25 G 5/800 onto the agar in the scanning tray (i) The scanning tray is filled with dPBS solution, enough to cover the tissue sample, which is to serve as acoustic coupling in which the transducer will be partially submerged during the scanning process Figure 13 illustrates an image of a prepared porcine small bowel placed under a μUS scanner 3.3.2 Inclusion of Fiducial Marker into Porcine Small Bowel Tissue Experiments conducted to detect changes in the porcine small bowel tissue sample over a period of time requires the same region of the tissue to be scanned multiple times As the tissue is submerged in dPBS, only anchored to the agar by Microlance™ Orange 25 G 5/800 , it cannot be assumed that the tissue is neither being displaced nor undergoing a biological change such as tissue necrosis Experiments using ex vivo mouse large bowel cells have 558 Thineskrishna Anbarasan et al Fig 13 Prepared porcine small bowel tissue pinned to the agar layer in the scanning tray for μUS scanning The tissue has been perfused, transected on its longitudinal axis and flipped over to expose the internal surface for μUS scanning shown significant cellular migration [7] This highlights the need to develop a method to determine potential tissue migration which could affect μUS scanning through the comparison of reconstructed B-scan images Polybead® Microspheres 90.0 μm (Polysciences, Inc., Pennsylvania, USA) were used as fiducial markers in the porcine small bowel tissue samples to be compared over a number of separate scans An Omnifix®-F Solo ml syringe (Braun, Melsungen, Germany) connected to a Microlance™ Green 21G 1.500 (Becton, Dickson and Company, New Jersey, USA) was used to inject Polybead® Microspheres 90.0 μm in the region of interest of the tissue sample The angle of penetration of the Microlance™ Green 21 G 1.500 should be approximately 15 from the surface of the tissue (see Note 9) 3.3.3 Preparation of Porcine Small Bowel Tissue for Scanning Whilst Perfusion To develop a tissue phantom which mimics the in vivo environment accurately requires a setup which allows for simultaneous perfusion and scanning Two major issues have to be considered in the development of such a system: (1) ensuring the cannulation is intact within the mesenteric artery throughout the μUS scan; (2) minimizing the effects of the perfusing fluid on the μUS transducer Steps in preparing such a phantom are similar to those described in Subheading 3.3.1, apart from certain changes discussed below (see Note 12) (a) The cannulation process should be attempted with the tissue sample placed directly on the agar surface in the scanning tray instead of the on the working surface to eliminate the need to move the cannulated tissue and risk the cannula becoming dislodged or damaging the vessel (see Notes and 8) Small Bowel Microultrasound 559 Fig 14 Schematic cross section of porcine small bowel pinned to agar layer in a scanning tray for μUS scanning with simultaneous perfusion of dPBS solution The transected superficial layer of the small bowel exposes the superficial mesenteric vessel through which the perfusing dPBS solution could interfere with the μUS transducer This issue is minimized by ligating the superficial mesenteric vessel to prevent leakage of dPBS solution in the path of travel of the transducer (b) Once, the superficial surface of the small bowel is transected, it will expose the mesenteric vessel supplying the superficial surface through which the perfusing dPBS solution will leak, interfering with the μUS transducer affecting the reconstructed B-scan images Though leakage cannot be avoided completely, its effect can be minimized by ligating the superficial mesenteric vessel as illustrated in Fig 14 to divert the perfusing dPBS to the periphery of the scanning tray instead of directly in the path of travel of the μUS transducer Ligation of the superficial mesenteric vessel is done using arterial forceps to clamp the vessel perpendicular to its axis (see Note 13) 3.3.4 Preparation of Working Solutions (a) Phosphate buffered saline (PBS) (DNase-, RNase-, and protease-free filtered through a 0.2 μm filter; pH: 7.4 Æ 0.1 contains: 11.9 mM phosphates; 137 mM NaCl; 2.7 mM KCl, Fisher Scientific UK Ltd) is diluted with distilled water with a volume ratio of 1:10, boiled at a setting of 350  C for and cooled to room temperature (b) 1% (w/w) Agar granular powder, general purpose grade (Fisher Scientific UK Ltd.) is mixed with water distilled and degassed by boiling at 350  C for 10 while stirring with a magnetic stirrer (c) g of M™ Glass bubbles K series are mixed with 10 ml of distilled water and filtered through an epidural flat filter, with Luer-Lok™ connection (PORTEX®, Smiths Medical, Kent, UK) 3.3.5 Setup of Scanning Tray The scanning tray consists of two layers, prior to being filled with PBS for scanning, as illustrated in Fig 560 Thineskrishna Anbarasan et al (a) An acoustic absorber sheet cut according to the dimensions to fit into the transparent container, is placed inside the container (b) The agar solution prepared as described in Subheading 3.3.3, step is poured into a transparent container containing an acoustic absorber sheet, covered and left to cool for 15 before being placed in the fridge for h (see Note 14) Notes During μUS scanning slight vibrations experienced by the μUS scanning system can affect the accuracy of the scan data The DPR500 Dual Pulser/Receiver must be switched off prior to elevating the μUS transducer from the acoustic coupler, dPBS solution, in the scanning tray to avoid damaging the μUS transducer Air bubbles, which have a tendency to form on the surface of the μUS transducer, could affect the accuracy of μUS scanning Hence, using a lens cleaning paper, the surface of the μUS transducer is gently cleaned prior to immersion in the acoustic coupling liquid After determining the start point of the region of interest for μUS scanning, pinning a needle adjacent to it allows for accurate positioning of the μUS transducer for scanning In the μUS stepping scanner system, derivation of acquisition start point time from the MDO3014 mixed domain oscilloscope has to be done carefully to define the scanning window so as to exclude only the transducer signal and avoid loss of tissue signal Decortication of the superficial layer of the mesentery from porcine small bowel tissue has to be done with particular attention to the underlying vasculature to avoid rupturing it Cannulation should be attempted in the proximal aspect of the mesenteric vessel before it bifurcates into the vessels supplying the superficial and deep surface of the small bowel, as illustrated by the schematic in Fig 12 To avoid transection of the mesenteric vessel during cannulation, the degree of approach should be optimally kept at 15 It must be ensured that there are no air bubbles present within the tubing or syringe prior to infusion to avoid potential interference of air bubbles with μUS scanning 10 Upon achieving successful cannulation of the mesenteric vessel of the tissue sample, the flaps of the butterfly valve should be Small Bowel Microultrasound 561 immediately pinned to the working surface to prevent any potential dislodging or transection of the vessel 11 BD ml Luer-Lok ™ syringe with red food dye solution to determine if cannulation is successful should be depressed gently to establish perfusion at low pressures, as otherwise the risk of vessel rupture is increased 12 Perfusor® has a maximum capacity of 60 ml which, at a perfusion rate of 200 ml/hr., would allow for a μUS scan duration of only 18 Unless a syringe perfusor with a larger capacity is used the time constraint has to be factored into the design of μUS scan experiments 13 Transection along the longitudinal axis of the superficial layer of the porcine small bowel tissue must be commenced only upon confirming that the tip of the scissors does not come into contact with the deep small bowel layer risking damage to its mucosal surface 14 After 3–5 μUS scan experiments, the agar layer in the scanning tray should be changed as multiple pin depressions on the agar layer would affect determination of the reference point in the scan image References Foster FS, Hossack J, Adamson SL (2011) Micro-ultrasound for preclinical imaging Interface Focus 1:576–601 Ødegaard S, Nesje LB, Lærum OD, Kimmey MB (2012) High-frequency ultrasonographic imaging of the gastrointestinal wall Expert Rev Med Devices 9:263–273 Sankey EA, Dhillon AP, Anthony A, Wakefield AJ, Sim R, More L, Hudson M, Sawyerr AM, Pounder RE (1993) Early mucosal changes in Crohn’s disease Gut 34:375–381 Technology Assessment Committee, Liu J, Carpenter S, Chuttani R, Croffie J, Disario J, Mergener K, Mishkin DS, Shah R, Somogyi L, Tierney W, Petersen BT (2006) Endoscopic ultrasound probes Gastrointest Endosc 63:751–754 Swindle MM, Makin A, Herron AJ, Clubb FJ Jr, Frazier KS (2011) Swine as models in biomedical research and toxicology testing Vet Pathol 49:344–356 Cobbold RSC (2006) Ultrasound image arrays Foundations of biomedical ultrasound Oxford University Press, New York, pp 492–497 Nelson SA, Li Z, Newton IP, Fraser D, Milne RE, Martin DM, Schiffmann D, Yang X, Dormann D, Weijer CJ, Appleton PL, N€athke IS (2012) Tumorigenic fragments of APC cause dominant defects in directional cell migration in multiple model systems Dis Model Mech 5:940–947 ... sensor and enabling continuous monitoring Miniaturization: Increasingly, biosensors are being miniaturized for incorporation into equipment for a wide variety of applications including clinical... Xiao-Ling Guo, Qian Wang, Jin-Lian Li, Ji-Wen Cui, Shi Zhou, and Su-E Hao xv vii xix 13 23 41 55 71 89 113 125 135 153 xvi 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Contents All-Electrical... Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand JINGHUA YU  School of Chemistry and Chemical Engineering, University of Jinan, Jinan, China LINGWEN ZENG  Institute