Day 2 :
Keynote Forum
Kevin L Lear
Colorado State University, USA
Keynote: Biomedical and environmental sensing applications of lateral wave vector response to refractive index
Time : 10:00-10:40
Biography:
Kevin L Lear is a Professor and Associate Director at Colorado State University. He completed his PhD as an Office of Naval Research Fellow at Stanford University. His subsequent work on vertical cavity surface emitting lasers at Sandia National Laboratories led to commercialization of this technology at Micro Optical Devices, Inc., where he was the Chief Technology Officer. He joined CSU in 1999 as the Rockwell Anderson Associate Professor where his research extended from semiconductor optoelectronics to include a variety of refractive index and fluorescence optical biosensors, microfluidics, and biomedical applications.
Abstract:
Optical guided wave biosensors transduce molecular binding or chemical changes via effects of refractive index variation on the optical propagation constant in the guiding structure. In some cases, the change in propagation constant is manifested through alterations in coupling conditions, such as for grating and surface plasmon resonance (SPR) devices where the coupling angle is a function of refractive index. Other common approaches, including Mach-Zehnder interferometers (MZI) and ring-resonators, rely on change in longitudinal phase that is the integral of the longitudinal component of the wave vector in the waveguide. Much less common are sensing devices that exploit the change in the lateral component of the wave vector in response to refractive index. However, the sensitivity of evanescent decay constants in claddings and large ratiometric changes in field amplitude that are available at distances of several decay lengths make sensing lateral wave vector changes intriguing. The local evanescent array coupled (LEAC) sensor uses variation in evanescent field coupled to an integrated photo detector array to transduce small changes in upper cladding refractive index to changes in photocurrent. Similar to other refractive index sensors, the LEAC technology is a platform that can be adapted to a variety of applications depending on the chemistry in the exposed cladding. When the LEAC waveguide core is patterned with antibodies, it can function as an immunoassay. More recently hydrophobic polymer coatings have been used to allow the same underlying sensor structure to measure benzene and other aromatic hydrocarbon contaminants in water in the ppb range.
Keynote Forum
Mouad Lamrani
Applied Research & Photonics Inc., USA
Keynote: Biomaterials as biosensors for microbial biomarkers in human tears and saliva: Proof of concept
Time : 11:00-11:40
Biography:
Anis Rahman is known for his work on dendrimer based photonics and terahertz technology. He has completed his MS and PhD from Marquette University (Milwaukee, WI) and Postdoctoral Research Position at Columbia University, USA. He has contributed more than 100 publications and conference presentations and has produced 12 patents. Currently, he is the President and Chief Technology Officer of Applied Research & Photonics (ARP), a Harrisburg, PA based company. He is also the Chair-elect of the division of small chemical businesses of the American Chemical Society.
Abstract:
In this presentation, we will enumerate the important role played during last decade by biosensing and bioelectronics in developing new diagnostic methodologies and tools. A comparative study of different existing techniques measuring biological signals is also announced. Accordingly, in this work we introduce proof of concepts of biosensing in eye tears and saliva using different biomaterials. Hence, using biomarkers present in human tear and saliva as medium of pathology detection leads to development of accurate diagnosis and early recognition of disease. This concept of biomarker biosensor using biomaterials has potential possibility of rapid, point-of-care diagnostic. Our preliminary results showed that the biomaterial biosensor was capable of detecting microbial biomarkers at low concentrations. The biomaterial biosensor was also considerably faster at detecting the target molecules, completing the analysis in short time.
Keynote Forum
Darryl J Bornhop
Vanderbilt University, USA
Keynote: Backscattering interferometry marries aptamer-based assays to enable quantitation ofnerve agent metabolites and human cytomegalovirusin urine at clinical relevant levels
Biography:
Bornhop is Professor of Chemistry at Vanderbilt University and is an international expert on the development of lanthanide chelates for contrast detection of cancers.
Abstract:
Backscattering interferometry (BSI) is a method for the detection of molecular interactions with unique capabilities and numerous advantages important to the near patient setting. These include high sensitivity, low sample volume and “label free†and either free solution or tethered probe operation. Based on an optical train consisting of the same components of a CD player; a laser, an object and a detector BSI’s simple optical train can be easily ruggedized and miniaturized. BSI provides quantitative binding data at femtomolar (fM) sensitivity with <15% coefficient of variation on clinical sample matrices such as serum, saliva and urine. In our presentation we will describe the principals of operation for BSI and then show two examples of aptamer enabled BSI detection relevant to near patient diagnosis. The first example will be the quantification of methylphoshonate metabolites of two nerve warfare agents and the second, detection of two major structural proteins of human cytomegalovirus which could serve as biomarkers of disease. We will show that our aptamer BSI assay for “VX acid†and “GB acid†yielded low nanomolar LOQ’s with high selectivity and minimal cross reactivity. In the case of cytomegalovirus, picomolar LOQ’s urine of were achieved using an aptamer to glycoprotein B, “gB†or the viral protein “pp65â€. The probe volume LOQ of BSI is several thousand target aptamer species, opening the avenue to early detection of CMV. An approach to constrain environmental noise in BSI will also be presented that is anticipated to lead to a bench top BSI that can be used widely by the unskilled operator.
- Day 02
Session Introduction
Yulia V Gerasimova
University of Central Florida, USA
Title: Split deoxyribozyme sensors for highly selective analysis of nucleic acids
Time : 14:00-14:30
Biography:
Yulia Gerasimova obtained her PhD from Institute of Chemical Biology and Fundamenal Medicine (Russia). She is currently an Assistant Professor at University of the Central Frolida Chemistry Department. Her reserach interests are in the field of nucleic acid-based sensors for nucleic acid analysis, which can be applied for disease diagnostics, food and water quality monitoring, as well as for biochemistry research assays. Dr. Gerasimova has published more than 20 papers in leading journals in this field.
Abstract:
Deoxyribozymes (Dz) are small catalytic DNA molecules, which can catalyze a variety of chemical reactions. Due to their structural versatility, biocompatibility, signal amplification ability and relatively low cost, Dz are widely used as scaffolds for biosensor design. Here we present a split Dz (sDz) approach for nucleic acid sensors: a Dz is divided into two subunits, which are not catalytically active in the absence of a nucleic acid target due to spatial separation; when target is present, the two subunits are brought in proximity, and the catalytic core is re-formed. As a result, target-inducable signal is generated and can be monitored for target detection and quantification. The binary design enables great selectivity because each of the two short probe-analyte hybrids is very sensitive to even a slight imperfection in the sequence of the analyzed nucleic acid. Using this approach, we have designed sDz sensors targeting rRNA of Escherichia coli, Mycobacterium tuberculosis and M. absesses, which are important human pathogens. We have demonstrated that the sensors are capable of differentiation between single nucleotide substitutions (SNSs) in the analyzed sequences. Therefore, it is possible to use sDz for SNSs and strain genotyping, as well as for drug susceptibility testing of bacterial pathogens. sDz sensors can be also employed for rRNA maturation monitoring and mutation analysis. The sensors can generate either fluorescent signal or color change. In their later implementation, sDz sensors can be used for point-of-care diagnostics of bacterial pathogens. The work was partially supported by NIH R21 HG004060 and NIAID R15AI10388001A1.
Victoria Wang Yue
Hill-Rom Services Private Limited, Singapore
Title: Capacitive sensor for respiratory monitoring
Time : 14:30-15:00
Biography:
Victoria has completed her PhD at the age of 28 years from National University of Singapore. She is a Mechanical Engineer of Hill-Rom, a leading provider of medical technologies for the health care industry including hospital beds, patient lifts, and non-invasive therapeutic products. She has published more than 6 papers in reputed journals or books. She also achieved first prize in project competition in Stanford - Singapore Biodesign program focused on Medtech innovation.
Abstract:
Continuous patient vital sign monitoring is prevalent in hospitals nowadays. It helps to significantly reduce caregiver’s work load. Out of all the vital signs, respiratory rate is seldom continuously monitored. Nurses usually manually estimate the respiratory rate from counting within thirty seconds. This could lead to both inaccuracy and discontinuity of monitoring. Even if respiratory rate is captured in some cases, what is used in hospital nowadays is bulky and invasive devices which brings discomfort to patients. Clinically speaking, respiratory rate is equally important as compared to other vital signs. Respiration monitoring can help to predict health crises, more specifically, failures in many organ systems. Therefore, there is an emerging clinical need to provide better respiratory monitoring solution. This presentation will present an idea that provides cost-effective and non-contact solution that is well-suited for patients who have a difficulty or uneasiness to use the contact RR monitoring devices. Patient's cintinously tracked RR data can be sent wirelessly to the caregivers or integrated to hospital’s EMR system. Hill-Rom has in-house developed a capacitive sensor that can be placed underneath a foam or air-filled mattress. The sensor is able to sense patient position, pressure inside the air bladders. Besides, the same sensor can be used to calculate patient’s respiratory rate by sensing the incremental body displacements caused by breathing. A sophisticated algorithm has been developed to overcome the lower SNR issue. 96% accuracy rate (+/-2 bpm) has been achieved in our preliminary test study for various use cases on five human subjects.
George Tsekenis
Biomedical Research Foundation of the Academy of Athens, Greece
Title: The BIOFOS-LoC: Micro-ring resonator-based biophotonic system for food analysis
Time : 15:00-15:20
Biography:
Will be updated shortly....!
Abstract:
Current methodologies for detection of food contamination, based on heavy analytical tools, cannot guarantee a safe and stable food supply. The reasons are the complexity, the long time-to-result (2-3 days) and the cost of these tools, which limit the number of samples that can be practically analyzed at food processing and storage sites. The need for screening tools that will be still reliable but simple, fast, low-cost, sensitive and portable for in-situ application is thus urgent. The BIOFOS project, an EC-funded FP7-ICT project, addresses this need through a high-added value, reusable biosensor system based on optical interference and lab-on-a-chip (LoC) technology. To do this, BIOFOS combines the most promising concepts from the photonic, biological, nanochemical and fluidic parts of LoC systems, aiming to overcome limitations related to sensitivity, specificity, reliability, compactness and cost issues. BIOFOS relies on the ultra-low loss TriPleX photonic platform in order to integrate on a 4x5 mm2 chip 8 micro-ring resonators, a VCSEL and 16 Si photodiodes, and achieve a record detection limit in the change of the refractive index of 5•10-8 RIU. To support reusability and high specificity, it employs aptamers as biotransducers, targeting at the reusability of the chips for 30 successive cycles. Advanced surface functionalization techniques were used for the immobilization of aptamers, and new microfluidic structures were introduced for the sample pre-treatment and the regeneration process. At the same time, novel techniques for the optimization of target analyte binding and increase in the recorded signal were developed, which can be applied to all relevant miniaturized biosensor systems that aim to quantify a biological recognition event which is most of the times almost at the system noise level by amplifying it. BIOFOS assembled the parts in a 5x10x10 cm3 package for a sample-in-result-out, multi-analyte biosensor. The system is in the process of being validated in real settings against antibiotics, mycotoxins, pesticides and copper in milk, olive oil and nuts, aiming at detection below the legislation limits and time-to-result only 5 minutes. It also targets lactose in lactose-free milk. Based on the reusability concept, BIOFOS also aims at reducing the cost per analysis by at least a factor of 10 in the short- and 30 in the mid-term, paving the way for the commercial success of the technology.
Chi Lin
Arizona State University, USA
Title: Development toward a multi-marker and label-free platform sensor technology using electrochemical impedance spectroscopy and nanomaterials
Time : 15:40-16:00
Biography:
Chi Lin is currently pursuing his PhD from Arizona State University through the School of Biological and Health Systems Engineering under the mentorship of Dr. Jeffrey T LaBelle. He is the leader of four projects under the LaBelle’s Lab: Dry eye sensor for advance tear diagnostics, LLC, Saliva glucose sensor, TOUCH tear glucose sensor and Tunable EIS multimarker detection team. He is specialized in the design and development of electrochemical sensors for various applications.
Abstract:
In complex diseases such as cancer and cardiovascular diseases (CVD), there has been an increasing need to measure multiple markers simultaneously for disease management and detection as a single biomarker cannot sufficiently represent the series of intricate physiological phenomenon. Comparing to traditional multi-marker testing methods that often utilize sensor arrays, Electrochemical Impedance Spectroscopy (EIS) offers a rapid, label-free, and ultrasensitive means to measure multiple markers simultaneously on just a single sensor. A novel analytical algorithm using the imaginary impedance is introduced as a proof of concept for multi-marker detection. By using this algorithm, an optimal frequency at which the resulting impedance best correlate to target’s concentrations can be identified, offering an orthogonal detection approach in addition to the specific binding between a target and its molecular recognition element (MRE). The algorithm is applied to show feasibility in detecting HDL and LDL, two strong predictors of CVD risk levels, simultaneously on a gold disc electrode sensor at 3.09 Hz and 175.8 Hz, respectively. To solve potential signal aliasing in future development of a multi-marker sensing platform, the algorithm is used to evaluate the tuning effect of nanoparticle conjugations onto the IL-12 antibody. Comparing to the control, it is observed that 5 nm, 10 nm, and 20 nm gold nanoparticles can shift the optimal frequency by 64.2 Hz, 4.05 Hz, and -14.09 Hz, respectively, and alter the full width half maxima by 295 Hz, 79.9 Hz, and 10.73 Hz, respectively.
RoozbehAbedini-Nassab
Duke University, USA
Title: Automated single cell arrays based on magnetophoretic circuits
Time : 16:00-16:20
Biography:
As a key member in Magnetophoretic Circuits project, RoozbehAbedini-Nassabis a Ph.D. Student at Duke University. His recent works are published in high impact journals such as Nature Communications, Advanced Materials, and Advanced Functional Materials.
Abstract:
Single-cell Array (SCA) systems are emerging tools in medical research with applications in cancer therapy, immunology, and in studying cellular heterogeneity. However, existing SCAs are neither sufficiently large nor automated to enable the study of rare cell behaviors and cell-cell interactions. In order to achieve these goals, we developed a novel SCA composed of magnetophoretic integrated circuit elements to manipulate and store single living cells, in analogous to random access memories (RAM), which store electrons (data) in computer systems. These integrated circuits are based on overlaid magnetic and metallic patterns fabricated on silicon or glass substrates, coated by non-fouling PEOGMA layer. The driving force for transporting magnetically labeled cells to desired locations on the chip is provided by a rotating magnetic field, which shifts the local minima of the potential energy landscape along controlled directions, dragging the magnetically labeled cells along desired paths. The new platform allows us to build significantly larger cell-based RAMs, capable of organizing>10,000 single-cells with operation times of less than an hour. We have the ability to store single-cells or cell pairs on specific storage sites and perform phenotypic study, over time. Moreover, we can selectively release them for follow-on transcriptomic analyses.
Biography:
Daniel Pesantez focused his PhD research on BioMEMS sensors at the College of Nanoscale Science and Engineering, State University of New York. Currently, he is a Senior Scientist at Medtronic Diabetes, working in next generation sensing technologies research and development. Dr. Pesantez serves as reviewer and technical arbitrator for reputed scientific peer reviewed journals as has authored several papers and patents on biosensors and microfabrication.
Abstract:
Detection and measurement of physiological relevant analytes is an essential step for diagnosis and monitoring of health and fitness conditions. The integration of lithography and microfabrication has allowed the miniaturization of medical devices, biosensors and applications in the fields of biological, environmental science, sports and fitness through clinical medicine. The miniaturization of biosensors has enabled new discoveries, diagnoses, and treatments by creating novel devices, systems, and analyses. Biosensors are biophysical devices which can detect the presence of specific analytes (e.g. sugars, proteins, hormones, pollutants, toxins). They are also capable of measuring the quantities of these specific substances in the environment and human body. For example, Diabetes is a health condition where biosensors have made a significant contribution. According to the National Report from the Center of Disease Control and Prevention, Diabetes affects more than $29 million people in the USA alone. The total medical cost for diabetics is around $245 billion dollars a year. Glucose biosensors are a great tool helping diabetic patients to monitor and manage their disease more efficiently and effectively. New advances in these devices such as integrating redundancy and alternative sensing, algorithms and data analytics has allowed for better and more accurate monitoring and treatment of the disease.
Kevin L Lear
Colorado State University, USA
Title: Biomedical and environmental sensing applications of lateral wave vector response to refractive index
Biography:
Kevin Lear is a professor and associate director of biomedical engineering at Colorado State University. He received his PhD as an Office of Naval Research Fellow at Stanford University while researching quantum tunneling devices. His subsequent work on vertical cavity surface emitting lasers at Sandia National Laboratories led to commercialization of this technology at Micro Optical Devices, Inc. where he was the chief technology officer. He joined CSU in 1999 as the Rockwell Anderson Associate Professor where his research extended from semiconductor optoelectronics to include a variety of refractive index and fluorescence optical biosensors, microfluidics, and biomedical applications.
Abstract:
Optical guided wave biosensors transduce molecular binding or chemical changes via effects of refractive index variation on the optical propagation constant in the guiding structure. In some cases, the change in propagation constant is manifested through alterations in coupling conditions, such as for grating and surface plasmon resonance (SPR) devices where the coupling angle is a function of refractive index. Other common approaches, including Mach-Zehnder interferometers (MZI) and ring-resonators, rely on change in longitudinal phase that is the integral of the longitudinal component of the wave vector in the waveguide. Much less common are sensing devices that exploit the change in the lateral component of the wave vector in response to refractive index. However, the sensitivity of evanescent decay constants in claddings and large ratiometric changes in field amplitude that are available at distances of several decay lengths make sensing lateral wave vector changes intriguing. The local evanescent array coupled (LEAC) sensor uses variation in evanescent field coupled to an integrated photo detector array to transduce small changes in upper cladding refractive index to changes in photocurrent. Similar to other refractive index sensors, the LEAC technology is a platform that can be adapted to a variety of applications depending on the chemistry in the exposed cladding. When the LEAC waveguide core is patterned with antibodies, it can function as an immunoassay. More recently hydrophobic polymer coatings have been used to allow the same underlying sensor structure to be used to measure benzene and other aromatic hydrocarbon contaminants in water in the ppb range.
Mandana Veiseh
Palo Alto Research Center, USA
Title: Cell-based biosensors and bioelectronics for health and environment: From polysensing to deconvoluting complexity and heterogeneity
Biography:
Mandana Veiseh completed dual PhD in Materials Science & Engineering and Nanotechnology at University of Washington, and postdoctoral studies at Fred Hutchinson Cancer Research Center and Lawrence Berkeley National Laboratories (LBNL). With recent roles as area manager of Bioengineered Devices and Systems at the Electronic Materials and Devices Laboratory of PARC and affiliate scientist in Biosciences area of LBNL, her multidisciplinary publications (garnering >1430 citations), inventions, and awards including selection as 2015 USFOE-NAE have contributed to the development of new scientific venues and the launch and success of three biotech startups, where she acted as scientific co-founder, co-inventor and advisor.
Abstract:
Recent decades have witnessed many advances in development of cell-based biosensors (CBBs) for addressing clinical, environmental and toxicological problems. While some could be useful means for diagnosis, prognosis and treatments of lethal diseases such as metastatic cancers or for precision medicine, far too many have not translated into on-site use. Contributing reasons are sensitivity of cells to micro- and nano-environmental alterations that result in noise and distortion from optimum condition, lower specificity of cell-based- compared to nucleic-acid- or antibody-based sensors, and longevity concerns. These CBBs and their integrated bioelectronics, if devised and targeted to address the noted shortcomings, are capable of providing comprehensive functional information and insights into the mechanisms of actions upon cellular interaction with bioactive stimuli (such as bioprobes, drugs, and environmental challenges) or during expression of useful biomarkers. The complexity, heterogeneity, and multi-parameter nature of these processes require development of high-performance and field-ready technologies suitable for handling and analyzing large numbers of heterogeneous samples and providing quantitative__ideally digitized, predictive, and integrated readouts from living cells. This talk presents technologies that have advanced our understanding, including multi-omics, imaging, and label-specific chemical assays, followed by some examples of missing links for proper tackling of aggressive disease states regardless of the culprits. In end, the promise of polysensing technologies for capturing multiplexed biomarkers and temporal/spatial correlations that would otherwise be missed by static and label-specific measurements on fixed cells or summing of single mode biomarkers sensed by separate equipment or at different times will be discussed.
Thu-Hoa Tran-Thi
Research Director IRAMIS/UMR France
Title: Terbium (III) as a luminescent probe for the detection of tuberculosis biomarkers
Biography:
Thu-Hoa Tran-Thi received her PhD degree in chemistry in 1983 at the University of Paris XI in Orsay. Since 1982, she has been a researcher of the CNRS at CEA-Saclay and is currently CNRS Director of Research. She presently leads the “Chemical Sensors” team in the CEA-CNRS NIMBE unit and is also the scientific counsellor of ETHERA, a CEA-CNRS spin-off. She has directed 90 students including 16 PhD students and 28 postdoctoral fellows. She has published 90 articles and has 11 patents.
Abstract:
Tuberculosis still infects 8.8 million and kills 1.3 million persons per year. Early diagnosis of the infection would reduce the disease’s effects. Many teams over the world have worked to improve in selectivity and time-consumption the standard diagnostic methods based on sputum analysis and bacteria culture. Cepheid has commercialized an Xpert MTB/Rif test with the result in 2 hours. Despite its reduced price for developing and high TB burden countries, the system still suffers from a drawback: the calibration needs to be performed by a trained technician using specialized equipment. Therefore, the search for easy-to-use, low-cost and selective tests remains a challenge. Non-invasive detection of a specific metabolite marker of Mycobacterium tuberculosis (M-Tb) present in cultures and patients’ breath is a promising method. A few metabolites of M-Tb in culture supernatants were found to be specific for M-Tb, including nicotinic acid (NA), methyl phenylacetate, p-methyl anisate, methyl nicotinate, and 2-methoxy biphenyl. Interestingly, NA could also be detected in the breath of patients with active tuberculosis. Based on these findings, our objective has been to propose a new easy-to-use method for NA detection in biological samples and in particular in a breath condensate. The method is based on analysis of the luminescence increase of Tb3+ complexes in the presence of NA due to the energy transfer from the excited ligand. We will show the limit of detection and the strategy developed to circumvent interferences from other metabolites. The method’s cost is evaluated and compared with the WHO-endorsed Xpert MTB/RIF test.
Biography:
Bornhop is Professor of Chemistry at Vanderbilt University and is an international expert on the development of lanthanide chelates for contrast detection of cancers.
Abstract:
Backscattering interferometry (BSI) is a method for the detection of molecular interactions with unique capabilities and numerous advantages important to the near-patient setting. These include high sensitivity, low sample volume and “label free”and either free-solution or tethered-probe operation. Based on an optical train consisting of the same components of a CD player; a laser, an object and a detector BSI’s simple optical train can be easily ruggedized and miniaturized. BSI provides quantitative binding data at femtomolar (fM) sensitivity with < 15% coefficient of variation on clinical sample matrices, such as serum, saliva, and urine. In our presentation we will describe the principals of operationfor BSI and then show two examplesof aptamer-enabled BSI detection relevant to near-patient diagnosis. The first example will be the quantification of methylphoshonate metabolites of two nerve warfare agents, and the second, detection of two major structural proteins of human cytomegalovirus which could serve as biomarkers of disease. We will show that our aptamer-BSI assay for “VX-acid” and “GB-acid” yielded low nanomolar LOQ’swith high selectivity and minimal cross-reactivity. In the case of cytomegalovirus, picomolar LOQ’surineof were achieved using an aptamer to glycoprotein B, “gB” or the viral protein “pp65”. The probe volume LOQ of BSI is several thousand target-aptamer species, opening the avenue to early detection of CMV. An approach to constrain environmental noise in BSI will also be presented that is anticipated to lead to a bench-top BSI that can be used widely by the unskilled operator.
Delphine Gourdon
Cornell University, USA
Title: 3D conducting polymer platforms for electrical control of protein conformation and cell functions
Biography:
Delphine Gourdon is an Assistant Professor in the Departments of Materials Science & Engineering and Biomedical Engineering at Cornell University. She earned her Ph.D. in Physics from the Swiss Federal Institute of Technology in Lausanne before becoming a postdoctoral fellow at Chem EUC Santa Barbara in Jacob’s Israelachvili’s lab. She was then appointed as a lecturer at the Swiss Federal Institute of Technology of Zurich in the Materials Department before joining Cornell in 2009. She is a co-author of 30+ publications. Her research interests include tumorous cellular mechanotransduction, 2D and 3D microfabricated surfaces for engineering cell functions, and biolubrication.
Abstract:
Fibronectin (Fn) is a prominent extracellular matrix glycoprotein that regulates cell adhesion, migration, differentiation and even pro-angiogenic secretion during processes such as embryonic development and tissue remodeling. Conformational changes of Fn are critically important in guiding these cell functions and have, for example, been linked to pathologies ranging from fibrosis to cancer. I will report the fabrication of novel three dimensional (3D) macroporous scaffolds made from poly (3, 4-ethylenedioxythiophene): poly (styrenesulfonate) (PEDOT:PSS) via an ice-templating method. These scaffolds offer tunable pore size and morphology, and are electrochemically active. When applying a potential, the scaffolds uptake ions that generate reversible changes in electronic conductivity through their entire volumes, which in turn enable precise control over adsorbed protein(especially Fn) conformation, as assessed by Fluorescence Resonance Energy Transfer. Moreover, these scaffolds support the growth of mouse fibroblasts for seven days and show electrical control over both cell adhesion and secretion of vascular endothelial growth factor, a crucial signaling protein involved in angiogenesis (vascularization). Collectively our data show that we have achieved physiologically-relevant 3D platforms with precise control of cell adhesion and pro-angiogenic secretion over large volumes and long cell culture times. As such, these platforms represent a new tool for biological research with many potential applications in basic research, tissue engineering, and regenerative medicine.
NaHyun Cho
Stony Brook University, USA
Title: Ordered DNA Fragmentation using soft lithography and Amplification for Next Generation Sequencing
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:
Current Next Generation Sequencing (NGS) technology starts with randomly fragmented DNA from whole genomic DNA. Because of this randomness, all DNA fragments need to sequence massive parallel reads in order to know the whole sequencing. In this study, we try to cut DNA fragments into 10-15 kbps using soft lithography technology because one of the NGS platforms is Pacific Biosciences’ RS, able to read larger size fragments, up to 15 kilo base pairs, quickly. Also, as an ultimate goal we will try to keep the DNA fragments in the orders from the surface, so the DNA reads do not need to be sequenced several times. In previous studies, we stretched DNA on PMMA (Poly Methyl Methacrylate) substrate and the stretched DNA could be linearly cut with soft lithography by applying DNase I enzyme. After cutting the DNA on the substrate, in order to sequence the DNA fragments with NGS technology, the DNA fragments are taken from the surface and placed in a solution base. We dissolved the PMMA substrate and fragmented DNA fragments together and separated the DNA fragments using a Phenol-Chloroform Isoamyl (PCI) extraction procedure. The principle of separating DNA with PCI mixture is based on solubility differences between organic and aqueous liquids. DNA is a negatively charged, hydrophilic bio-polymer because of its negatively charged phosphate groups. On the other hand, PMMA is a non-charged polymer that is dissolved in chloroform. By dissolving the PMMA surface, it is possible to separate DNA from the surface using liquid-liquid phase separation (Organic phase: Aqueous phase). For the data processing, confocal microscopy was used to take images of cut DNA on the PMMA surface. Gel electrophoresis and bioanalyzer were conducted to confirm the distribution of the DNA fragments. Finally, PacBio RS II which is the one of the long-read Next-Generation sequencing platforms was used to confirm quality and quantity of the fragmented DNA from surfaces.