Samir M. Iqbal, Ph.D. - US grants

The objective of this proposal is to develop new modalities for the isolation and detection of selective proteins (biomarkers), by using aptamer-protein interactions in nano/microfluidic channels/chambers with multiplexed nanoscale electrodes and on-chip data processing. To accomplish the goals, a coherent strategy of fabrication and modeling will be adopted: (1) Development of functionalized membranes for isolation of low-abundant disease biomarkers, (2) Design and development of a bio-chip with individually-addressable nano-electrodes, made with high-throughput nanoimprint lithography and functionalized with aptamers for multiplexed detection of biomarkers, (3) Development of novel and rapid fabrication of nano/microfluidic channels, (4) Modeling, analysis and characterization of the electronic properties of biomarker-aptamer interactions measured between the nano-electrodes, and, (5) Real-time low-power noise-free read-out circuit with sequential addressing, actuation, measurement & data analysis of the recognition sites.

INTELLECTUAL MERITS: This proposal will transform and create a new area ?proteonics?, building up on the advances in ?proteomics? and ?molecular electronics?. The activities leverage from the molecular scale devices and the in vitro aptamer-protein interactions, and are extendible to a host of other applications. The ideas will overcome bottlenecks of expensive and serial fabrication in molecular electronics and provide alternate to the labor-intensive, poorly-sensitive and lengthy protocols of proteomics. The novel polymer nano/microfluidics will provide proper conditions to retain protein expression and functionality. On-chip circuit will lead the way to prototype point-of-care proteonic bio-chips. The nano-electrodes will provide a 3-D interaction volume for aptamer-protein binding, resulting in higher sensitivity and signal-to-noise ratio than those for planar morphologies. The approach will also overcome sensitivity limitations by removing the effects of device doping, geometry, dimensions, and fluidic environments. The proposed strategies will innovatively transform and revolutionize a number of disciplines: (1) Rapid nano-manufacturing for bio-sensing, (2) Multiplexed detection of disease markers using various aptamers, (3) Ultrasensitive on-chip electrical detection of biomarkers and analysis for early disease detection, (4) Mask-less production of novel nano/microfluidics.

BROADER IMPACT: The proposal has direct applications in other biosensor domains, e.g. gene expression analysis, virus/pathogen detection and whole blood analysis. The variations of the propose technology can transform biomolecular sensing with better disease intervention strategies, improved statistical confidence and real-time detection. The PI has engaged women graduate students and minority undergraduate/high school students in his research lab. Innovative educational endeavors will be pursued with this proposal: (1) Development of a graduate course on nano-bio devices, (2) Seminars/Demos/Lab-tours focused on research involvement and retention of undergraduates, (3) One-week summer camp for high school students (primarily African-American and Hispanic) from Arlington school district, integrating MEMS/Nano research and biology concepts, (4) Interactive website/blog for the projection/exposure/discussion of the state of the art in research, (5) Saturday morning live-chat sessions to follow-up/engage K-12 students and teachers, (6) Technology transfer studies to nurture entrepreneurship in students interested in real-world problems, (7) Development of international research collaborations for exchange of students from and to USA. The results of the proposed ideas will be disseminated through peer-reviewed articles, conferences and public media.

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)"

The objective of this research is integration of optical, electrical and mechanical systems at nano- and micro-meter scale, thus enabling novel biomedical, energy harvesting and structural health monitoring devices and systems, otherwise not possible. The approach is to use a wafer aligner and bonder system for precision alignment and bonding of a diverse set of substrates including semiconductor wafers, glass substrates, metals and polymers.

The intellectual merit lies in combining top-down and bottom-up fabrication techniques to pioneer new interfaces between semiconductor-based devices and biomolecules that can be tailored for specific applications, both as sensors and actuators / controllers of biological phenomena. The interrogation of bio-molecules and understanding of real cellular interactions require 3-D biocompatible structures, chambers and interfaces. Ranging in length scales from a few nanometers to many microns, inter and intra-cellular mechano-transduction signals play important roles in many aspects of cellular functions.

The proposed Precision Wafer Aligner / Bonder will be part of NanoFab at UT Arlington, which is an interdisciplinary resource open to scientists within and outside of the University. The Dallas-Forth Worth metropolitan region is home to more than 400 high tech institutions. As a user facility, the NanoFab will make the wafer aligner / bonder available 24/7 to these researchers and provide them training for usage. An annual workshop as well as an online discussion forum dedicated to 3-D integration will be established.

Objectives:

This proposal addresses a number of fundamental and important obstacles that have limited the utility of nanopore sensing technology. Specifically, nanopore size, surface composition and stability of the pores are addressed to broaden this technology to include important new areas, e.g. sequencing of genomes, as but one of many examples. To help expedite progress in this area, our objective involves fabrication and thorough evaluation of a new approach to nanopore sensor technology. Specifically, we propose construction of artificial pores in which both the size and surface chemistry of the pores are precisely controlled over a wide range of pore sizes. For this purpose, a novel combination of thermal processing, followed by pulsed plasma chemical vapor deposition, will be used to shrink pore sizes controllably and reproducibly, while simultaneously varying surface chemistry. Availability of these molecularly engineered nanopores will hopefully overcome limitations currently encountered in analytical applications of this technology. An additional important objective involves extension of this technology to several new, high profile applications to be made available via our approach, e.g., selective differential detection by two oppositely chirally functionalized nanopores which will revolutionize chromatographic measurement of chiral compounds; similar schemes will be possible in many other cases.

Intellectual Merits of the Proposed Activity?

To date, nanopore fabrication has focused primarily on low-throughput serial approaches, with little use of bottom-up technology. In general, key issues such as stability of nanopore/fluid interfaces, reproducibility of nanopore surface properties, extended pore stability and the need for robust chemical functionalization of the nanopores remain. The ready availability of mechanically stable nanopores, having a range of well-defined diameters and surface chemistries, as described in this proposal, represents a transformative advance in this area. New insights will be gained from selective interactions in nanopores, providing quantitative handles to evaluate the molecular responses of ligands and to define novel, chemical means of interrogating targeted analytes. This will stimulate additional studies: control of translocation times of analytes through the pores (an immensely important present problem) and the use of chemistry and size differentiated nanopore arrays. This innovation will also help overcome and replace the present labor-intensive and low-throughput fabrication methods.

Broader Impacts of the Proposed Activity?

The proposed project will impact many areas that depend on the confluence of sciences and engineering. Examples include design of bio-inspired systems, sensors for environment and living systems, etc. The basic principles involved can be integrated into all levels of education. Graduate and undergraduate (UG) students will be engaged and introduced to exciting new dimensions of analytical chemistry, biochemistry and solid-state fabrication through development of a cross-listed course module on the bio-nano interface. The research outcomes will be also used to develop integrative participatory modules at our presently conducted Summer Camps (for middle/high-school students) and Girlgeneering Camps (for female high school students) to attract future adults to STEM careers. These outreach endeavors will be pursued: (1) Seminars/lab-tours for involvement and retention of UGs in research; (2) Engaging minority students through the McNair Fellows program; (3) Dynamic Facebook presence for the projection/exposure/discussion of the research; (4) Engagement of K-12 students and teachers through live webcasts. The results of the proposed research and education endeavors will be disseminated not only through peer-reviewed articles and conferences, but also through public media (radio, newspaper, weblogs, public displays). UTA Chemistry participates in the local State Fair. UTA has the largest digital planetarium in the Metroplex, with extremely heavy K-12 traffic. We plan to develop a small clip on nanopore sensors.

The high mortality rate of patients with invasive and metastatic cancer has changed little over the past few decades. Early detection is crucial for better treatment of cancer and to increase survival rates. Traditional diagnostic approaches fail to detect some types of cancers at very early stages. Bladder cancer is usually silent in early stages resulting in diagnosis at late and often incurable stages. Occasionally, the symptoms of both benign conditions and bladder cancer are nonspecific and very similar. In about 85% of cancer patients, there may be red blood cells present in the urine. But the same symptoms may be the result of an infection or inflammation in the urinary tract (kidney, bladder, prostate). This proposal aims at providing a non-invasive, low-cost, highly sensitivity, and ultra-specific approach using solid-state microdevices and biochemical functionalization of chip surfaces. The functionalization will target the molecules that are overexpressed on tumor cells. Automation of the data acquisition and analysis will be done to determine physical behavioral differences and biomarker expression levels between tumor and normal cells. The molecules chosen for targeted detection of tumor cells will add significant value as indicators and predictors of the outcomes of the treatment. This proposal will change how cancers, and especially bladder cancer, are diagnosed. The experiments will be done first with cultured cells, then with cells isolated from the blood of animals bearing human bladder cancer xenografts, and finally with real patient clinical samples. The multi-disciplinary team will integrate the novel technology that will provide educational opportunities for students on the whole continuum of K-Grad. Graduate and undergraduate students will be engaged and introduced to exciting new dimensions of cell biology, biochemistry and solid-state fabrication through development of a cross-listed course module on the cell-nano interface. The research outcomes will be also used to develop participatory modules at College of Engineering summer camps to attract future adults to STEM careers. The results, data and outcomes of the research and education endeavors will be disseminated not only through peer-reviewed articles and conferences, but also through social and public media.

The novelty of the proposal lies in three elements: first, a special class of probe molecules called aptamers will be used. Aptamers can be reversibly denatured, and these will therefore provide a mechanism for the reversible release of tumor cells in their native states. Second, the nanotextured substrates will provide biomimetic environment to examine the cell behavior. Third, dynamic behavior of tumor cells will be used to measure the temporal evolution of cell-cell interactions over days at single-cell or sub-cellular scales. This new tumor detector will serve as a non-invasive cell type reporter (without "staining" the cell), and as a cell culture substrate with prescribed behavior of cells for certain level of biomarker overexpression. Currently such a platform does not exist. The technological integration described in this proposal may therefore provide early means of identifying remission or metastases, and even give some insights into how many and what types of metastases may be present in a given sample.