Characterization of Nanoparticles Using Solid State Nanopores

Solid state nanopores are widely used in detection of highly charged biomolecules like DNA and proteins. In this study, we use a solid state nanopore based device to characterize spherical nanoparticles to estimate their size and electrical charge using the principle of resistive pulse technique. The principle of resistive pulse technique is the method of counting and sizing particles suspended in a fluid medium, which are electrophoretically driven through a channel and produce current blockage signals due to giving rise to a change in its initial current. This change in current is denoted as a current blockage or as a resistive pulse. The information from these current blockage signals in case of nanopore devices and spherical nanoparticles helps us to look at the properties of each individual nanoparticles such as size, electrical charge and electrophoretic mobility. In this thesis, two spherical nanoparticles of different sizes and different surface charge groups are used: Negatively charged 25 nm iron oxide nanoparticle with – COOH surface group and positively charged 53 nm polystyrene nanoparticle with – NH2 surface group. Nanopores used in these studies are about twice the nanoparticle size. These nanopores were fabricated by various fabrication techniques such as, Focused ion beam milling and ion beam sculpting method. The current blockage events produced by these two nanoparticles were measured as a function of applied voltage. The parameters extracted from the current blockage events, such as the current drop amplitudes and event duration are analyzed to estimate the size and electrical charge of the nanoparticles. Estimation of drift velocity of the nanoparticle and diffusion coefficient are also discussed. The estimated size is then compared to the nanoparticle size obtained from dynamic light scattering technique. Stable nanoparticles are widely used in biological and pharmacological studies and understanding the behavior of these nanoparticles in a nanopore environment would make a significant contribution to the studies at the nanoscale

Beta-lactam resistance in gram-negative bacteria isolated in India

The most important resistance mechanism to beta -lactam antibiotics is the plasmid- mediated beta -lactamase and the common criterion for the epidemiology of these enzymes is the determination of their biochemical characteristics. Surveys of plasmid- encoded beta-lactamases of Gram -negative bacteria used to investigate their relative clinical importance have been poorly performed and rarely conducted outside the developed world.A Survey of uropathogenic strains and of Salmonellae and Shigellae, isolated in South India in 1984 revealed a higher incidence of ampicillin resistance (Minimum Inhibitory Concentration [MIC] >10mg/1) than had ever been reported before (Enterobacteriaceae 80.9%, Salmonellae 90 %, Shigellae 66 %). Only the enterobacterial strains showed any significant resistance to the first generation cephalosporin, cephaloridine (MIC >10mg/1). However, 65.7% of the Salmonella, strains were cefuroxime resistant. Cefuroxime resistance in these Salmonella, strains was accompanied by the widespread distribution of the novel OXA -El like enzyme with more hydrolytic activity against the drug, even though other resistance mechanisms may play subsidiary role. A small proportion of all species conferred resistance to third generation cephalosporins. In the individual species, there was a very high incidence of ampicillin resistance (E.coli 77 %; Klebsiella 69 %) and cephaloridine resistance (E.coli 57 %; Klebsiella 96 %). Many of the ampicillin resistant strains harboured either auto -transferable or mobilisable plasmids (41.8 %). Characterisation of the plasmid DNA from the E.coli transconjugants revealed the existence of 37 different plasmids types. The transconjugants from Klebsiella, Salmonella and Shigella possessed fewer plasmids types than those from E.coli. Most plasmids possessed resistance genes to aminoglycosides and to six or more ii drugs. Beta -lactamase studies revealed that TEM -1 was the most predominant enzyme in all transconjugant strains followed by OXA -1, SHV -1, TEM -2, OXA -2 and the novel enzyme SAR -2. The SAR -2 enzyme was fully characterised and had a higher pI (8.3) than any previously characterised plasmid- mediated beta -lactamase. It had a broad -spectrum activity with the molecular weight of 36000. In addition, the unusual observations of E.coli strains producing both the PSE -1 and PSE -2 beta - lactamases and strains hyperproducing the TEM -1 were made and these strains were studied further.The development and mechanisms of resistance to beta -lactam/beta -lactamase inhibitor combinations (ampicillin and clavulanic acid) have been performed with laboratory strains possessing the ampicillin resistance plasmids R1, R1010 and extended -broad spectrum beta -lactam resistance plasmids. The results show that challenge with clavulanic acid alone did not affect the expression or integrity of the beta -lactamase whereas challenge with the combination of ampicillin and clavulanic acid caused radical changes - i the expression of the beta -lactamase. In some cases there were multiple copies of genes which resulted in hyperproduction of TEM -1 enzyme and this was sufficient to resist the combinations. Similarly, elevated SHV -1 enzyme production resulted in a resistance mechanism with no concurrent reassortment of the plasmid R1010. Unfortunately, these variants also conferred resistance to second and third generation cephalosporins. The enzymes TEM -3, TEM -5 and TEM -7 were not hyperproduced but the corresponding strains were stable against the combination at higher inoculum density. Importantly, the SHV -1 beta -lactamase had become active against cefotaxime as it was able to hydrolyse the drug. Evidence of this type of resistance (hyperproduced TEM -1 and SHV -1 enzymes) to clavulanic acid is now emerging in clinical practice

Loop Tiling in the Presence of Exceptions

Exceptions in OO languages provide a convenient mechanism to deal with anomalous situations. However, many of the loop optimization techniques cannot be applied in the presence of conditional throw statements in the body of the loop, owing to possible cross iteration control dependences. Compilers either ignore such throw statements and apply traditional loop optimizations (semantic non-preserving), or conservatively avoid invoking any of these optimizations altogether (inefficient). We define a loop optimization to be xception-safe, if the optimization can be applied even on (possibly) exception throwing loops, in a semantics preserving manner. In this paper, we present a generalized scheme to do exception-safe loop optimizations and present a scheme of optimized exception-safe loop tiling (oESLT), as a specialization thereof. oESLT tiles the input loops, assuming that exceptions will never be thrown. To ensure the semantics preservation (in case an exception is thrown), oESLT generates code to rollback the updates done in the advanced iterations (iterations that the unoptimized code would not have executed, but executed speculatively by the oESLT generated code) and safely-execute the delayed iterations (ones that the unoptimized code would have executed, but not executed by the code generated by oESLT). For the rollback phase to work efficiently, oESLT identifies a minimal number of elements to backup and generates the necessary code. We implement oESLT, along with a naive scheme (nESLT, where we backup every element and do a full rollback and safe-execution in case an exception is thrown), in the Graphite framework of GCC 4.8. To help in this process, we define a new program region called ESCoPs (Extended Static Control Parts) that helps identify loops with multiple exit points and interface with the underlying polyhedral representation. We use the popular PolyBench suite to present a comparative evaluation of nESLT and oESLT against the unoptimized versions

Homeostasis: Design and Implementation of a Self-Stabilizing Compiler

Mainstream compilers perform a multitude of analyses and optimizations on the given input program. Each analysis (such as points-to analysis) may generate a program-abstraction (such as points-to graph). Each optimization is typically composed of multiple alternating phases of inspection of such program-abstractions and transformations of the program. Upon transformation of a program, the program-abstractions generated by various analyses may become inconsistent with the modified program. Consequently, the correctness of the downstream inspection (and consequent transformation) phases cannot be ensured until the relevant program-abstractions are stabilized; that is, the program-abstractions are either invalidated or made consistent with the modified program. In general, the existing compiler frameworks do not perform automated stabilization of the program-abstractions and instead leave it to the compiler pass writers to deal with the complex task of identifying the relevant program-abstractions to be stabilized, the points where the stabilization is to be performed, and the exact procedure of stabilization. In this paper, we address these challenges by providing the design and implementation of a novel compiler-design framework called Homeostasis. Homeostasis automatically captures all the program changes performed by each transformation phase, and later, triggers the required stabilization using the captured information, if needed. We also provide a formal description of Homeostasis and a correctness proof thereof. To assess the feasibility of using Homeostasis in compilers of parallel programs, we have implemented our proposed idea in IMOP, a compiler framework for OpenMP C programs. We present an evaluation which demonstrates that Homeostasis is efficient and easy to use.Comment: Accepted for publication in ACM TOPLAS. 58 pages, 36 figures. Patent granted in India. US Patent published. For associated code, see https://github.com/anonymousoopsla21/homeostasi

Development of Biomimetic Interfaces and Their Applications.

This dissertation details strategies for the fabrication of sophisticated biofunctional materials and their use in biomedical and biotechnological application. These unique biointerfaces were designed by integrating biological entities with synthetic polymers and extensively characterized using surface analytical tools. The first part of this dissertation focuses on the immobilization of specific moieties that render surfaces biomimetic. Synthesis of reactive polymers, poly(4-formyl-p-xylylene-co-p-xylylene) and poly(4-heptadecafluoronononyl-p-xylylene-co-p-xylylene) was accomplished via chemical vapor deposition (CVD) polymerization. These reactive polymer coatings enabled the immobilization of proteins and oligosaccharides via chemoselective carbonyl-hydrazide coupling reaction. On the other hand, an alkyne-functionalized polymer coating, poly(4-ethynyl-p-xylylene-co-p-xylylene) was synthesized for the conjugation of proteins, saccharides and cell-adhesive oligopeptides via alkyne-azide “click” reaction, in a spatioselective manner. These platforms were further used for surface-directed adhesion of human endothelial cells. Another application of reactive polymers was directed towards the fabrication of polymer coatings, which mimic endothelial cells with respect to nitric oxide generation for cardiovascular stents. Photo-reactive polymer coatings were deposited using CVD polymerization and used to incorporate Cu(II) ligated cyclen (1,4,7,10-tetraazacyclododecane) onto the surface of a stent. These catalytic sites containing copper generated NO from endogenous S-nitrosothiols present in blood, and the measured NO flux approached physiological ranges. These coatings attempt to solve the problems of restenosis and thrombosis associated with the placement of coronary artery stents. In the second part of the dissertation, a chemically-defined polymer was fabricated, which supported long-term human embryonic stem (hES) cell cultures, for the first time, in the presence of several different culture media. Polymer, poly[2-(methacryloyloxy)ethyl dimethyl-(3-sulfopropyl)ammonium hydroxide] sustained the culture of hES cells for at least 25 passages in mouse fibroblast conditioned medium, at least 15 passages in commercially-available human cell conditioned medium and at least 10 passages in defined StemPro medium. Throughout the study, hES cells expressed undifferentiated cell markers, retained a normal karyotype and remained pluripotent. Development of a standardized culture matrix for hES cells represents a significant step towards future clinical applications of hES cells. Taken together, these approaches offer novel solutions for target applications in tissue engineering, biomedical devices and microfluidics and further expand our toolbox of strategies for creating biologically-relevant surfaces.Ph.D.Chemical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/64816/1/nhima_1.pd

Engineering, Characterization and Directional Self-Assembly of Anisotropically Modified Nanocolloids

Along with traditional attributes such as the size, shape, and chemical structure of polymeric micro-objects, control over material distribution, or selective compartmentalization, appears to be increasingly important for maximizing the functionality and efficacy of biomaterials. The fabrication of tri- and tetracompartmental colloids made from biodegradable poly(lactide-co-glycolide) polymers via electrohydrodynamic co-jetting is demonstrated. The presence of three compartments is confirmed via flow cytometry. Additional chemical functionality is introduced via the incorporation of acetylene-functionalized polymers into individual compartments of the particles. Direct visualization of the spatioselective distribution of acetylene groups is demonstrated by confocal Raman microscopy as well as by reaction of the acetylene groups with azide-biotin via ‘click chemistry’. Biotin–streptavidin binding is then utilized for the controlled assembly and orientation of bicompartmental particles onto functionalized, micropatterned substrates prepared via chemical vapor deposition polymerization.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/83480/1/812_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/83480/2/smll_201001695_sm_suppl.pd