Single Molecule Electrophoresis and Optical Detection Using Thermoplastic Nanofluidic Devices: An Experimental and Simulation Study

Nanofludic devices provide a great platform for single molecular analysis. The unique phenomena in nanoscale gained such interest in investigating the single molecular behavior in nanochannels. Sizes less than 200 nm in one or two-dimensional structures have lead to fascinating observations not accessible in microscale. When a single molecule translocates through a nanotube it interacts with channel walls by adsorption/ desorption, van der Waals interactions and hydrophilic interactions providing a mechanism for separation without any extra additives. Moreover, double layer thickness governed by the background electrolyte plays a vital role. We report single molecular electrophoresis phenomena in nanochannels and nanoslits based on experiment and simulation studies. This will provide the guidance for sequencing DNA by clipped single monomer nucleotides based on their unique time-of-flight (ToF) signatures when electrokinetically driven through a nanotube. The nanofluidic devices were fabricated in thermoplastic devices using mixed micro-scale and nanoscale methodologies. We also report a novel bonding methodology at low temperature using thermoplastic devices with high glass transition substrate sealed to a low glass transition cover plate. This approach prevents distorted nanochannels specially when fabricating nanochannels less than 50 nm to facilitate DNA stretching studies. Genomic mapping of single molecules has gained attention significantly during the last decade. Genomic mapping of DNA molecules facilitated region-specific drug development. We study the development of a nanofluidic-based sensor to monitor chemotherapy responses in cancer patients by stretching their genomic DNA in nanochannels and identifying the specific damage sites

Monitoring the progression of metastatic breast cancer on nanoporous silica chips

Breast cancer accounted for 15 per cent of total cancer deaths in female patients in 2010. Although significant progress has been made in treating early-stage breast cancer patients, there is still no effective therapy targeting late-stage metastatic breast cancers except for the conventional chemotherapy interventions. Until effective therapy for later-stage cancers emerges, the identification of biomarkers for the early detection of tumour metastasis continues to hold the key to successful management of breast cancer therapy. Our study concentrated on the low molecular weight (LMW) region of the serum protein and the information it contains for identifying biomarkers that could reflect the ongoing physiological state of all tissues. Owing to technical difficulties in harvesting LMW species, studying these proteins/peptides has been challenging until now. In our study, we have recently developed nanoporous chip-based technologies to separate small proteins/peptides from the large proteins in serum. We used nanoporous silica chips, with a highly periodic nanostructure and uniform pore size distribution, to isolate LMW proteins and peptides from the serum of nude mice with MDA-MB-231 human breast cancer lung metastasis. By matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and biostatistical analysis, we were able to identify protein signatures unique to different stages of cancer development. The approach and results reported in this study possess a significant potential for the discovery of proteomic biomarkers that may significantly enhance personalized medicine targeted at metastatic breast cancer

06. 2005 Seventeenth Annual IMSA Presentation Day

https://digitalcommons.imsa.edu/class_of_2005/1004/thumbnail.jp

2005 Seventeenth Annual IMSA Presentation Day

The Student Inquiry and Research Program fosters the development of students as highly skilled and integrative problem finders, problem solvers, and apprentice investigators, all skills required to succeed in the global workplace of the 21 Century.https://digitalcommons.imsa.edu/archives_sir/1017/thumbnail.jp

Experimental Evaluation of Uranyl Transport into Mesoporous Silica Gel using Fluorescence

This research investigated parameters that can affect the use of nanoporous silica gel as a media for accumulating a detectable amount of uranium. The unique fluorescence of the Uranyl (UO22+) ion was used to evaluate the transport kinetics and accumulation within silica gel in a static fluid and under pressure driven flow. The addition of fluid flow decreased the time constant from on the order of an hour to approximately 2s with a very low fluid velocity of 0.36cm/s. The 0.36cm/s fluid velocity was found to be the critical velocity above which there was no gain in time constant. A table top instrument was developed that can detect trace amounts of uranium in solution. The table top instrument was used to investigate how the time constant depends on the uranyl concentration, which led to the development of a new time-based method for quantifying the uranyl concentration. The time-based method of detection uses a preset threshold and, based on the time it takes to reach that threshold, the concentration in the water sample can be determined. The lifetime of uranyl in complex with silica increased to approximately 120us, allowing for gated detection and background discrimination. In addition to the fluorescent contaminants, competing cations were tested to determine how they affect the fluorescence and transport kinetics of the uranyl. The cations tested were Mn2+, Ca2+, Mg2+, Na+, K+, and Li+. The result shows that within the natural concentrations, Mg2+, Na+, and K+ did quench the fluorescent of the uranyl ions by collision quenching. The time constant was also examined in the presence of each cation and showed that Ca2+, Mg2+, Na+, and K+ decreased the adsorption time constant. Future studies in this area should be directed toward the development of a portable version of the instrument

Isolation, sequencing, and characterization of four transmissible antibiotic resistance plasmids captured from bacteria in stream sediments

Self-transmissible plasmids are key vectors in the transfer of resistance, catabolic, and other genes among bacteria native to environments such as streams and wetlands. The evolution of antibiotic resistance in particular is known to be powerfully affected by conjugative plasmid transfer due to the ease in which some plasmids can be horizontally transferred into a broad range of host bacteria and their ability to exchange mobile genetic elements that often contain antibiotic resistance genes. In this study, we captured tetracycline resistance plasmids from stream sediments impacted by agricultural runoff. We selected for resistance plasmids using tetracycline, an antibiotic commonly used in agricultural operations, due to the numerous neighboring cattle pastures and poultry farms. We hypothesized that stream sediment is a “hot spot” for horizontal gene transfer due to the use of antibiotics in agricultural operations combined with runoff into streams. Selective pressures exerted on gut and fecal bacteria of farm animals may select for antibiotic resistance genes that can be horizontally transferred to native stream sediment bacteria when runoff events occur. We characterized four transmissible, tetracycline resistance plasmids: the 71 kb IncP-1β plasmid pEG1-06, the 121 kb IncA/C2 plasmid pCCRT11-6, and the 59 kb IncP-9 plasmids pCCP1 and pCCP2. We built upon and improved the methods developed for the preparation of plasmid DNA for sequencing using 2nd and 3rd generation DNA sequencers, hybrid genome assembly, annotation, and analysis. We demonstrated this process by assembling the four plasmid genomes into single, circular contiguous sequences and compared them to the closest related plasmids allowing us to classify their respective incompatibility groups, reveal the essential backbone and accessory genes present on the plasmid genomes including antibiotic resistance genes, and determine their similarity to the closest related known, existing plasmids

Microscopy and Analysis

Microscopes represent tools of the utmost importance for a wide range of disciplines. Without them, it would have been impossible to stand where we stand today in terms of understanding the structure and functions of organelles and cells, tissue composition and metabolism, or the causes behind various pathologies and their progression. Our knowledge on basic and advanced materials is also intimately intertwined to the realm of microscopy, and progress in key fields of micro- and nanotechnologies critically depends on high-resolution imaging systems. This volume includes a series of chapters that address highly significant scientific subjects from diverse areas of microscopy and analysis. Authoritative voices in their fields present in this volume their work or review recent trends, concepts, and applications, in a manner that is accessible to a broad readership audience from both within and outside their specialist area

Microfluidics and Nanofluidics Handbook

The Microfluidics and Nanofluidics Handbook: Two-Volume Set comprehensively captures the cross-disciplinary breadth of the fields of micro- and nanofluidics, which encompass the biological sciences, chemistry, physics and engineering applications. To fill the knowledge gap between engineering and the basic sciences, the editors pulled together key individuals, well known in their respective areas, to author chapters that help graduate students, scientists, and practicing engineers understand the overall area of microfluidics and nanofluidics. Topics covered include Finite Volume Method for Numerical Simulation Lattice Boltzmann Method and Its Applications in Microfluidics Microparticle and Nanoparticle Manipulation Methane Solubility Enhancement in Water Confined to Nanoscale Pores Volume Two: Fabrication, Implementation, and Applications focuses on topics related to experimental and numerical methods. It also covers fabrication and applications in a variety of areas, from aerospace to biological systems. Reflecting the inherent nature of microfluidics and nanofluidics, the book includes as much interdisciplinary knowledge as possible. It provides the fundamental science background for newcomers and advanced techniques and concepts for experienced researchers and professionals

Perspectives of Nuclear Physics in Europe: NuPECC Long Range Plan 2010

The goal of this European Science Foundation Forward Look into the future of Nuclear Physics is to bring together the entire Nuclear Physics community in Europe to formulate a coherent plan of the best way to develop the field in the coming decade and beyond.<p></p> The primary aim of Nuclear Physics is to understand the origin, evolution, structure and phases of strongly interacting matter, which constitutes nearly 100% of the visible matter in the universe. This is an immensely important and challenging task that requires the concerted effort of scientists working in both theory and experiment, funding agencies, politicians and the public.<p></p> Nuclear Physics projects are often “big science”, which implies large investments and long lead times. They need careful forward planning and strong support from policy makers. This Forward Look provides an excellent tool to achieve this. It represents the outcome of detailed scrutiny by Europe’s leading experts and will help focus the views of the scientific community on the most promising directions in the field and create the basis for funding agencies to provide adequate support.<p></p> The current NuPECC Long Range Plan 2010 “Perspectives of Nuclear Physics in Europe” resulted from consultation with close to 6 000 scientists and engineers over a period of approximately one year. Its detailed recommendations are presented on the following pages. For the interested public, a short summary brochure has been produced to accompany the Forward Look.<p></p&gt