Day 3 :
- Track 3: DNA Chips and Nucleic acid Sensors
Track 5: Photonic Sensor Technologies
Track 7: Biosensors for Imaging
Track: 11: BioMEMS/NEMS
Session Introduction
Amir Sanati-Nezhad
University of Calgary, Canada
Title: Workshop on whole plant-cell microfluidic-based biosensor for toxicity testing of environmental pollutants
Time : 10:00-11:00
Biography:
Will get updated shortly....!
Abstract:
The toxicity detection using real testing on human or animal is no longer an appropriate technique. Development of new technical methods for detecting toxic materials is highly demanded. A variety of non-animal methods are available for toxicity detection consists of in-vitro analysis of living cells and tissue cultures, microarray technology and computerized modeling. These methods can provide more reliable, faster and cheaper results. Various cells such as bacterial, mammalian and plant cells have been for the application in pharmacology, toxicology and environmental measurements. In this paper, we present a novel microfluidic-based whole cell biosensor to enable detection of environmental toxic substances through dynamics of oscillatory growth behavior of a whole plant cell in a high-throughput platform. Pollen tube as the fastest tip growing plant cells was used to demonstrate the performance of this plant-cell biosensor due to its extremely sensitivity to the external signals and environmental chemicals. The microfluidic platform was designed from the previously enhanced microfluidic device devised for chemical treatment of tip growing cells. The pollen grains were injected into the chip, conducted through the main chamber towards the growth microchannels and trapped at the entrance of microchannels. The individual pollen tubes grow along the microchannels and were subjected to chemical treatment. The growth of pollen tubes was observed under microscope before and after introducing the toxic medium (Aluminium). While for higher Al concentrations, the change of growth rate and the burst of pollen tube was useful to detect the Al concentration, for lower concentration of Al the dynamic behavior of pollen tube was exploited. The oscillatory dynamic growth includes both fundamental and higher modes of oscillation frequencies associated with growth. The effect of stress from toxic substance on variation of the fundamental and higher modes of dynamic oscillation of growth rate was used to detect the concentration of Al in the media. The experimental results show that for 20μM Al concentration and below, the drop of growth rate was not simply detected, though the variation or disruption of higher mode oscillation frequency in 20μM was simply detectable. The advanced waveform techniques of Fast Fourier transform (FFT) and window filtering techniques were used to identify the primary and secondary peak oscillation frequencies. For a sample pollen tube tested under 20μM Al concentration, the results of FFT analysis. When the cell is subjected to toxic environment, the behavior of the pollen tube was altered at entire range of dynamic growth and the power associated with change of all frequencies was used as a criterion of dynamic response in order to quantify the cell behavior under different concentration of toxic Al. The total power of its corresponding Fourier Transform integrated across all of its frequency components was calculated before and after treatment with Al toxic, each, in time series of 100s. The degree of toxicity (τ) was then defined as the ratio of spectral power of normal growth of pollen tube and spectral power of tube after treatment with Al toxic.
Hong-Yu Yu
South University of Science and Technology, China
Title: A novel leaky surface acoustic wave (LSAW) biosensor for label-free detection of hepatitis B surface antibody (HBsAb)
Time : 11:15-11:35
Biography:
Yu HongYu has been with the Department of EEE at SUSTC since 2011. He received a Bachelors of Engineering from Tsinghua University, he completed his Masters in Applied Science degree from University of Toronto and a PhD degree from National University of Singapore. He was at IMEC (Leuven Belgium) as a senior researcher in the Si process and device technology division. His current major research interests cover sustainable electronic devices, including low-power IC/memory devices, bio-electronics and green photonics/solar cell devices. He has authored and co-authored about 300 publications in the top tied international journals and conferences, with a total over 2000 citations (SCI) and with an H index of 28. He has been invited to give talks for more than 20 international conferences and also invited to write 4 book chapters. He also published and has been granted with 20 USA/EU patents. He is an IET fellow, and has received many awards.
Abstract:
As a potential biochemical sensing platform, leaky surface acoustic wave (LSAW) biosensor consists of a special orientation of a piezoelectric crystal and shows superb sensitivity, speed and reliability. In this work, a novel label-free LSAW biosensor for detecting hepatitis B surface antibody (HBsAb) is fabricated. The sensing area of LSAW is coated with 500nm thick gold membrane on a 100MHz LiTaO3 piezoelectric single crystal. Then the hepatitis B surface antigen (HBsAg) is immobilized on the surface of a gold electrode. The phase shift of LSAW is monitored to detect HBsAb, which increases the mass loading of LSAW by binding to immobilized HBsAg. A reference LSAW device is immobilized with bovine serum albumin (BSA) to block binding of HBsAb. This sensor shows great specificity and sensitivity in detecting HBsAb.
Jurgen Van Erps
Vrije Universiteit Brussel, Belgium
Title: Photonics-enhanced multi-functional labs-on-chips: from lab to fab
Time : 11:35-11:55
Biography:
Jürgen Van Erps has completed his Ph.D in 2008 at the age of 28 from the Vrije Universiteit Brussel (VUB), Belgium, and postdoctoral studies from the University of Sydney, Australia. Since 2013, he is professor at VUB. He authored or co-authored 41 SCI-stated papers and more than 90 papers in international conference proceedings. He is co-inventor of 3 patents. He serves as a reviewer for several international journals. He is a senior member of the SPIE, and member the OSA and the IEEE Photonics Society.
Abstract:
Although the development of labs-on-chips has witnessed tremendous progress in recent years, their applications have been limited to singular laboratory prototypes without widespread routine use in clinical or high-throughput applications. Most present-day lab-on-a-chip implementations rely on bulk optical instrumentation external to the microfluidic chip for read-out, monitoring or analysis. This implies that miniaturized portable systems are difficult to realize and there is a large demand for efficient, small and robust optical detection units to create photonics-enhanced labs-on-chips. With the development of polymer-based microfabrication techniques supported by replication technologies such as hot embossing or injection moulding, polymer microfluidic lab-on-a-chip devices hold tremendous opportunities for mass production. This paves the way towards low-cost disposable devices. In addition, polymers offer the advantage of material versatility, since a wide range of polymers is available with characteristics that are in accordance with the requirements for a specific application, such as good optical transparency, biocompatibility, desired chemical or mechanical properties, and suitability for system integration through embedding of components. We show our technology supply chain and our recent progress in the design, fabrication and proof-of-concept demonstration of integrated miniaturized photonics-enhanced biosensors for absorbance and fluorescence measurements as well as Raman spectroscopy. All systems combine high sensitivity with a relatively simple layout to ensure their manufacturability and robustness. In addition, the units can be reconfigured for sensing various molecules at different wavelengths paving the way towards multi-functional, low-cost, portable, robust, and, ultimately, disposable lab-on-a-chip systems that can be used in the field and for point-of-care diagnostic applications.
Yen Nee Tan
Institute of Materials Research and Engineering, Singapore
Title: Metallic nanoparticles biosensors: A colorful platform for detecting biomolecular interactions
Biography:
Yen Nee Tan received her PhD degree in Molecular Engineering of the Biological and Chemical Systems from the Singapore-MIT Alliance, National University of Singapore in 2008. She is currently leading the Bioinspired Materials Laboratory at the Institute of Materials Research and Engineering, A*STAR. She has filed 8 patents (3 granted and 1 licensed) and published several scientific papers in reputed journals (e.g., JACS, Anal Chem. etc.) in the area of bioassays development. She also serves as an editorial board member of the Austin Journal of Biosensors & Bioelectronics. Her recent awards include the Materials Research Contribution Award (2014), L’Oreal for Women in Science Singapore, Finalist (2013), Tan Kah Kee Young Inventors’ Award (2012), and AsiaNANO Young Researcher Award (2010).
Abstract:
Nobel metal nanoparticles (NPs) such as gold and silver, in the same size domain (<100 nm) as the biomolecules, are well suited for biosensing applications due to their unique optical properties arising from the localized surface plasmon resonance. We have developed three nanoplasmonic sensing to interrogate estrogen receptor (ER)-DNA interactions- an important transcriptional activity related to breast cancer biology. These assays exploit the interparticle distance-dependent plasmonic coupling and/or plasmon-induced fluorescent quenching as sensing elements. The first assay uses the citrate-anions capped AuNPs to probe the sequence-specific binding interactions of ER to various DNA sequences and to determine their binding stoichiometry without using labels, tedious sample preparation, and sophisticated instrumentation. This assay was further designed to couple with the aggregation-induced emission luminogen to allow dual optical signal (i.e., colorimetric and fluorescent) detection in a single experiment. The second assay was founded on the de-novo design of segmented ER-response DNA element onto two sets of metal NPs conjugates with complementary short sticky ends, where ER serves as a stabilizer to retard the particle aggregation induced by base-pairing and charge screening. This protein binding-stabilization strategy is generic and reduces the risk of getting false positive results. The third assay was designed based on the concept of traditional DNA footprinting using DNase with the combinatorial use of DNA-modified AuNPs to enable fast colorimetric detection without hazardous radioactive-labeling and tedious assessment of cleavage pattern. This versatile AuNPs-based enzymatic assay can be used to monitor nucleases activity, screen nucleases inhibitor, detect DNA-binding proteins and determine DNA sequence specificity in a fast, sensitive and convenient way.
Biography:
Rai Sachindra Prasad after obtaining his PhD Degree (Electrical Engineering) from Indian Institute of Technology, Kharagpur, India, has published several papers in International journals and IEEE Int Conferences. He has worked as professor in several technical institutes in India and has widely travelled in Europe and USA. He is a reviewer of IEEE and other reputed journals and is a member of several editorial boards of journals. After retirement in 2013 his main research interests are in imaging techniques of human bio-field- specifically in invisible physical body.
Abstract:
The fact that thought is physical force has been well recognized but hardly translated in the sense of its transfer from one individual to another. In the present world of chaos and disorder with yawning gaps between right and wrong thinking individuals, if it is possible to transfer the right thoughts to replace the wrong ones, it would indeed be a great achievement in the present situation of the world. With advances in bio-field imaging techniques already achieved, an instrumentation scheme may be designed and implemented to realize this thought transfer phenomenon. This is bound to be extremely useful when properly used. The advancements already made in recording the nerve impulses in the brain, in Aura extraction through the human bio-field measurements using GDV/EPI techniques, and the latest research finding proving the phenomenon of an invisible physical body of human beings, it is conceivable that this may be used in society’s transformation. So far only clinical aspects in instrumentation for ‘brain-to-brain transfer’ have been explored which are of no worth in bringing a permanent change for peace and tranquillity in the present world. Presently, recording of EEG relies on capturing thought waves in the so called meditation mode, i.e. closing eyes in rest position in half-sleep conditions, while completely ignoring the roles played by pineal body, pituitary gland and ‘association’ areas. In this paper, the ideal procedure of meditation is defined and then the concepts of possible design aspects of instrumentation for brain–to-brain transfer are discussed.
NaHyun Cho
Stony Brook University, USA
Title: Ordered DNA Fragmentation on surfaces for NGS Sequencing
Time : 11:55-12:10
Biography:
NaHyun Cho is a PhD candidate in Materials Science and Engineering at Stony Brook University in New York. She previously earned a BS in Engineering Chemistry and a ME in Materials Science and Engineering from at Stony Brook University. She spent two and half years in the field as a research engineer with LG Electronics in Seoul, South Korea, working in their crystalline solar cell R&D Center. Her current area of research is ordered DNA fragmentation on surfaces for next-generation sequencing. In order to further develop her research focus, she is a visiting student at both Cold Spring Harbor Laboratory and Brookhaven National Laboratory in New York.
Abstract:
Next Generation Sequencing (NGS) technology starts with 200 ~ 300 base pairs of random small DNA fragments that are cut from whole genomic DNA. For instance, human being’s genomic DNA is 3.2 X 109 base pairs, so assuming that the human DNA are cut into 300 base pairs fragments, there are 1.1X 107 fragments to sequence. Furthermore, in order to have statistically accurate sequencing data, massive parallel sequencing is required. It means that every genomic region of DNA fragments should be sequenced several times to reduce erroneous reads. It requires massive labor and time due to the randomness of DNA fragmentation in liquid solution. However, if it is possible to keep the order of cut DNA fragments instead of randomly cutting, the assembly of a contiguous sequence will be significantly simplified. In this study, we have researched non-random cutting and ordering of DNA on deposited and aligned polymer surfaces instead of typical liquid-based random DNA fragmentation in molecular biology. To have a controlled cutting process of DNA while keeping the ordering, we lineally anchored DNA molecules on a PMMA (Poly methyl Methacrylate) surface, so the DNA molecules are stationary. We cut the stretched DNA molecules on the surface with enzyme solution using a patterned PDMS (Polydimethylsiloxane) stamp having micron-sized features. Since the stamp has a grating structure, it enables the enzyme solution selectively to touch the anchored DNA molecules. Currently, we have studied the digestion mechanism of enzyme for the DNA molecules on the PMMA surface. We have used DNase I enzyme and NEBNext® dsDNA Fragmentase® from New England Biolabs because they nonspecifically cleave DNA molecules. Also, we have tried restriction enzymes such as XbaI and PvuI to understand the enzyme digestion mechanism on surface. For sample preparation, we use silicon wafers as substrates and spin cast PMMA solutions to cover the substrate with a thin film to anchor DNA molecules linearly. PDMS stamps were patterned using soft -lithography technology in Brookhaven National Lab, New York. For cutting the DNA on the surface, the stamp is coated with enzyme solution and placed in contact with the DNA molecules. After cutting, the DNA molecules and PMMA film are dissolved with organic solvent and the DNA is extracted using liquid-liquid separation (Organic phase: Aqueous phase). Confocal microscopy and Atomic force microscopy (AFM) were used to image the DNA molecules on the PMMA surface. Gel electrophoresis was conducted to confirm the distribution of the DNA fragments.
Hasan Aldewachi
Sheffield Hallam University, UK
Title: A Facile, Colorimetric Assay for DPP IV Activity and Inhibition Based on an Enzyme-Responsive Nanoparticle System
Time : 12:10-12:25
Biography:
Hasan Aldewachi did her undergraduate degree in the University of Mosul (Iraq),He then went to England for a Master degree in Pharmaceutical Analysis at the University of Sheffield Hallam. He published his Master Dissertation thesis in the Int. J. Pharm. Sci. Rev. Res. He is now doing a PHD at the University of the Sheffield Hallam under Dr. Philip Gardiner's supervision. His PHD project involves developing rapid and novel enzyme detection biosensors towards point of-care.
Abstract:
DPP IV is a transmembrane serine protease enzyme whose expression is up regulated in a variety of diseases therefore has been identified as potential diagnostic or prognostic marker for various tumors, immunological, inflammatory, neuroendocrine and viral diseases. Recently, DPP-IV enzyme has been recognized as a novel target for type II diabetes treatment where the enzyme is involved in the degradation of incretins. A variety of assays have been introduced for the determination of DPP-IV enzyme activity using chromogenic and fluorogenic substrates, nevertheless these assays either lack the required sensitivity especially in inhibited enzyme samples or they not suitable for in vivo analysis because of their low water solubility combined with time consuming sample preparation. In this study, novel strategies based on exploiting the high extinction coefficient of GNPs are investigated in order to develop fast, specific and reliable enzymatic assay. The presence of DPP IV could be detected by colorimetric response of peptide capped GNPs (P-GNPS) that could be monitored by a UV-Visible spectrophotometer or even the naked eyes. Very low enzyme activity can be measured using this approach. The P-GNPs when subjected to DPP IV showed excellent selectivity compared to different physiological serum proteins (lysozyme, thrombin, trypsin and human serum albumin). Furthermore, our new design could also be applied to the assay of DPP IV inhibition since the DPP IV inhibitors can suppress its hydrolytic action, and thus, this new methodology can be easily adapted to high throughput screening of DPP IV inhibitors.
Nageswara Lalam
Northumbria University, UK
Title: Real-time monitoring and localization of toxic pipeline leakages using distributed optical fibre sensor (DOFS) system
Biography:
Nageswara Lalam is a PhD researcher in school of engineering and environmental sciences, Northumbria University, United Kingdom. He received MS in wireless communication systems engineering from University of Greenwich, London, United Kingdom. He is working on distributed fibre optic sensor systems towards environmental monitoring. His current research interests includes, distributed optical sensors, stimulated Brillouin scattering and nonlinear optics.
Abstract:
Leakage of dangerous toxic acids from pipelines, flow lines, reactors, storages and oil wells is an severe impact on public. In fact, leakages of chemicals can be at the origin of toxic releases, which can have severe consequences on the installation as well as on the environment and nearby inhabitants. Industries are prompted to take all possible measures to reduce the occurrence of such catastrophic events by implementing additional technical safety barriers in order to prevent any potential danger. Pipeline leakages may have different origins, such as corrosion, fatigue, shocks, abnormal temperatures, extreme pressures, or excessive deformations caused by ground movement. In the case of liquefied or pressurized gases, leakages can be detected by the material deformation and rapid drop of temperature due to the evaporation of the released liquid and its evaporation gases or due to gas expansion. Brillouin scattering based distributed optical fibre sensor (DOFS) have unique features that have no match compared to other conventional sensing techniques. A single mode fibre cable is installed along the whole length of the pipeline then connected to a measurement system. DOFS system has an ability to detect the both temperature and micro-strain simultaneously with 1m spatial resolution and response time is less than 10s. As a result, we can prevent leakages from toxic acids pipelines before failure occurs.
Namik Akkilic
University of Twente, Netherlands
Title: Switching behavior of biomolecules attached to a responsive polymer brush
Biography:
Namik Akkilic completed his PhD at the Leiden University, Netherlandsas a Marie Curie Early Stage Researcher. The research was aimed at the control of single electron transfer events of a metalloprotein immobilized on a surface. Currently, he holds a postdoctoral position at the Twente University, Netherlands and works on responsive polymers as on-off switch for biosensor applications. He has published 7 papers and 1 book chapter to date.
Abstract:
Many investigations over the years have shown that the interaction of surface grafted polymer brushes with biomolecules like proteins, receptors has a great importance for a significant number of applications. Here we present on the design of a smart polymer brush/biomolecule architectures, produced via the “grafting to†approach. For this, individual protein molecules, labelled with the fluorophore ATTO488, were covalently attached to a single pH responsive poly(acrylic acid) (PAA) brush. Subsequently, total internal fluorescence microscopy (TIRF) was used to monitor intensity changes over time, when switching between low and high pH. We show that the fluorescence intensity of a single protein molecule shows an on-off switching behavior, controlled by the solution pH. Fluorescence intensity is quenched (off state) by 85% when the PAA chains are stretched at basic pH yet we observe an enhancement in the fluorescence (on state) when the polymer chains collapse at basic pH. Furthermore, we use the local density of optical states (LDOS) effect to predict the location of a molecule that is covalently (or electrostatically) attached to a polymer brush. Fluorescence lifetime was 3.5 ns when the polymer was stretched away from the grafting interface at basic pH, whereas the lifetime is quenched to just 2 ns at acidic pH. Moreover, we support our experimental results with numerical self-consistent field (nSCF) theory. Biomolecules can be either in (on state) or outside (off state) of the brush, and by fine-tuning the brush parameters and particle size it becomes possible to use this system as a biosensor.
Ying Wan
Nanjing University of Science and Technology, China
Title: Surface-initiated enzymatic polymerization based signal amplification strategies for electrochemical DNA sensors
Biography:
Ying Wan has completed her PhD at the age of 26 years from Shanghai Institute of Applied Physics in Chinese Academy of Science. After that, she continued her Postdoctoral studies from Toronto University School of Pharmacy. She is now a research scientist in Nanjing University of Science and Technology. She has published more than 20 papers in reputed journals.
Abstract:
Electrochemical DNA (E-DNA) sensors have great potential in point-of-care diagnosis because of their ability to produce a simple, accurate and inexpensive platform for DNA sensing. However, it is difficult to detect extremely low abundance of DNA biomarkers in clinical samples. Thus different signal amplification methods have been developed to improve the sensitivity of E-DNA sensors. In this paper, we developed an ultrasensitive E-DNA sensor based on the signal amplification efficiency of nanoprobe and surface-initiated enzymatic polymerization (SIEP). In this method, nanoprobe was fabricated by gold nanoparticles (AuNPs) modified with reporter probe DNA. Coupling with the nanoprobe, capture probe, which was immobilized on gold electrode, would form a “sandwich†with target DNA. Upon hybridization, nanoprobe could be bound to the electrode and then subjected to terminal deoxynucleotidyl transferase (TdT) catalyzed elongation of DNA strand at its 3′ terminal. During the terminal extension reaction, biotin labels are incorporated into the SIEP-generated long single-stranded DNA (ssDNA). Then specific binding of avidin modified – horseradish peroxidase (HRP) to the biotin label would lead to an enzyme turnover-based signal transduction. As there are hundreds of DNA probes on the nanoprobe, one hybridization event would generate hundreds of long ssDNA, resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide. By employing nanoprobe and TdT, we demonstrated that our E-DNA sensor has a detection limit of 10 fM and excellent differentiation ability for even single mismatches.
Manoj Kumar Patel
Jawaharlal Nehru University, India
Title: Nucleic acid biosensors: A smart approach towards pathogen detection
Biography:
Will get updated shortly....!
Abstract:
Nucleic acid biosensors (DNA biosensor) are recently gaining much intention in the field of biomedical science for point-of-care applications. Nucleic acid biosensing concepts are based on DNA hybridization, in which two complementary single stranded DNA hybridized and generate useful hybridization signals. DNA based biosensors has been reported for the detection of various pathogenic diseases like tuberculosis, meningitis and cholera. Cholera is an acute intestinal infection caused by ingestion of contaminated food or water. The Gram-negative bacterium Vibrio cholerae is responsible for the infection. The conventional diagnosis of cholera is based on microscopic examination, immunological test, biochemical test, and PCR. These tests are expensive, non-confirmatory, less sensitive and time consuming. Nucleic acid sequences are getting importance in nano-biosensing techniques for the detection of various diseases since the sequence has capacity to represent information, which directs the functions of a living thing. With this importance, DNA sequences have become indispensable for various applications in biological research such as DNA sequencing and clinical diagnostic etc. It is expected that nucleic acid biosensors may offer great advantages due to inherent sensitivity, selectivity and comparatively low detection cost. We report results of the studies related to the development of nucleic acid sensor based on magnesium oxides (MgO) nanoparticles, deposited via electrophoretic deposition (EPD) onto indium tin oxide (ITO) coated glass electrode followed by immobilizing complementary oligoneucleotide probe (ssDNA/MgO/ITO) with a terminal 5′-phosphate group and after hybridization with V. cholerae (O1) genomic DNA (dsDNA/MgO/ITO). The fabrication of electrodes has been confirmed using X-ray diffraction (XRD), Fourier transforms infrared (FTIR) spectroscopy and scanning electron microscopy (SEM). The results of electrochemical studies such as electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV) and differential pulse voltammetry (DPV) suggest that MgO/ITO electrode provides an increased effective surface area for the immobilization of DNA, thus, resulting in an improved electron transport between medium and electrode. The ssDNA/ MgO/ITO bioelectrode can detect the target DNA in the range of 100 to 500 ng/μL using hybridization technique in the presence of methylene blue as an electro-active indicator. The hybridization time is restricted to allow 5 min at 25oC. This DNA bioelectrode is stable for about 4 months when stored at 4°C.
Sina Aghili
Islamic Azad University, Iran
Title: Determination of effect factor for effective parameter on saccharification of lignocellulosic material by concentrated acid
Biography:
will be updated shortly...!
Abstract:
Tamarisk usage as a new group of lignocelluloses material to produce fermentable sugars in bio ethanol process was studied. The overall aim of this work was to establish the optimum condition for acid hydrolysis of this new material and a mathematical model predicting glucose release as a function of operation variable. Sulfuric acid concentration in the range of 20 to 60%(w/w), process temperature between 60 to 95oC, hydrolysis time from 120 to 240 min and solid content 5,10,15%(w/w) were used as hydrolysis conditions. HPLC was used to analysis of the product. This analysis indicated that glucose was the main fermentable sugar and was increase with time, temperature and solid content and acid concentration was a parabola influence in glucose production. The process was modeled by a quadratic equation. Curve study and model were found that 42% acid concentration, 15 % solid content and 90oC were optimum condition.