The development of direct ultra-fast PCR for forensic genotyping using short channel microfluidic systems with enhanced sieving matrices

There are situations in which it is very important to quickly and positively identify an individual. Examples include suspects detained in the neighborhood of a bombing or terrorist incident, individuals detained attempting to enter or leave the country, and victims of mass disasters. Systems utilized for these purposes must be fast, portable, and easy to maintain. The goal of this project was to develop an ultra fast, direct PCR method for forensic genotyping of oral swabs. The procedure developed eliminates the need for cellular digestion and extraction of the sample by performing those steps in the PCR tube itself. Then, special high-speed polymerases are added which are capable of amplifying a newly developed 7 loci multiplex in under 16 minutes. Following the amplification, a postage stamp sized microfluidic device equipped with specially designed entangled polymer separation matrix, yields a complete genotype in 80 seconds. The entire process is rapid and reliable, reducing the time from sample to genotype from 1-2 days to under 20 minutes. Operation requires minimal equipment and can be easily performed with a small high-speed thermal-cycler, reagents, and a microfluidic device with a laptop. The system was optimized and validated using a number of test parameters and a small test population. The overall precision was better than 0.17 bp and provided a power of discrimination greater than 1 in 106. The small footprint, and ease of use will permit this system to be an effective tool to quickly screen and identify individuals detained at ports of entry, police stations and remote locations. The system is robust, portable and demonstrates to the forensic community a simple solution to the problem of rapid determination of genetic identity.

Geographic provenancing of unprocessed cotton using elemental analysis and stable isotope ratios

Cotton is the most abundant natural fiber in the world. Many countries are involved in the growing, importation, exportation and production of this commodity. Paper documentation claiming geographic origin is the current method employed at U.S. ports for identifying cotton sources and enforcing tariffs. Because customs documentation can be easily falsified, it is necessary to develop a robust method for authenticating or refuting the source of the cotton commodities. This work presents, for the first time, a comprehensive approach to the chemical characterization of unprocessed cotton in order to provide an independent tool to establish geographic origin. Elemental and stable isotope ratio analysis of unprocessed cotton provides a means to increase the ability to distinguish cotton in addition to any physical and morphological examinations that could be, and are currently performed. Elemental analysis has been conducted using LA-ICP-MS, LA-ICP-OES and LIBS in order to offer a direct comparison of the analytical performance of each technique and determine the utility of each technique for this purpose. Multivariate predictive modeling approaches are used to determine the potential of elemental and stable isotopic information to aide in the geographic provenancing of unprocessed cotton of both domestic and foreign origin. These approaches assess the stability of the profiles to temporal and spatial variation to determine the feasibility of this application. This dissertation also evaluates plasma conditions and ablation processes so as to improve the quality of analytical measurements made using atomic emission spectroscopy techniques. These interactions, in LIBS particularly, are assessed to determine any potential simplification of the instrumental design and method development phases. This is accomplished through the analysis of several matrices representing different physical substrates to determine the potential of adopting universal LIBS parameters for 532 nm and 1064 nm LIBS for some important operating parameters. A novel approach to evaluate both ablation processes and plasma conditions using a single measurement was developed and utilized to determine the "useful ablation efficiency" for different materials. The work presented here demonstrates the potential for an a priori prediction of some probable laser parameters important in analytical LIBS measurement.

Evaluation of the evidential value of the elemental composition of glass, ink and paper by laser-based microspectrochemical methods

Elemental analysis can become an important piece of evidence to assist the solution of a case. The work presented in this dissertation aims to evaluate the evidential value of the elemental composition of three particular matrices: ink, paper and glass. In the first part of this study, the analytical performance of LIBS and LA-ICP-MS methods was evaluated for paper, writing inks and printing inks. A total of 350 ink specimens were examined including black and blue gel inks, ballpoint inks, inkjets and toners originating from several manufacturing sources and/or batches. The paper collection set consisted of over 200 paper specimens originating from 20 different paper sources produced by 10 different plants. Micro-homogeneity studies show smaller variation of elemental compositions within a single source (i.e., sheet, pen or cartridge) than the observed variation between different sources (i.e., brands, types, batches). Significant and detectable differences in the elemental profile of the inks and paper were observed between samples originating from different sources (discrimination of 87–100% of samples, depending on the sample set under investigation and the method applied). These results support the use of elemental analysis, using LA-ICP-MS and LIBS, for the examination of documents and provide additional discrimination to the currently used techniques in document examination. In the second part of this study, a direct comparison between four analytical methods (µ-XRF, solution-ICP-MS, LA-ICP-MS and LIBS) was conducted for glass analyses using interlaboratory studies. The data provided by 21 participants were used to assess the performance of the analytical methods in associating glass samples from the same source and differentiating different sources, as well as the use of different match criteria (confidence interval (±6s, ±5s, ±4s, ±3s, ±2s), modified confidence interval, t-test (sequential univariate, p=0.05 and p=0.01), t-test with Bonferroni correction (for multivariate comparisons), range overlap, and Hotelling's T2 tests. Error rates (Type 1 and Type 2) are reported for the use of each of these match criteria and depend on the heterogeneity of the glass sources, the repeatability between analytical measurements, and the number of elements that were measured. The study provided recommendations for analytical performance-based parameters for µ-XRF and LA-ICP-MS as well as the best performing match criteria for both analytical techniques, which can be applied now by forensic glass examiners.

The effect of iron oxide nanoparticles on the fate and transformation of arsenic in aquatic environments

Iron oxides and arsenic are prevalent in the environment. With the increase interest in the use of iron oxide nanoparticles (IONPs) for contaminant remediation and the high toxicity of arsenic, it is crucial that we evaluate the interactions between IONPs and arsenic. The goal was to understand the environmental behavior of IONPs in regards to their particle size, aggregation and stability, and to determine how this behavior influences IONPs-arsenic interactions. ^ A variety of dispersion techniques were investigated to disperse bare commercial IONPs. Vortex was able to disperse commercial hematite nanoparticles into unstable dispersions with particles in the micrometer size range while probe ultrasonication dispersed the particles into stable dispersions of nanometer size ranges for a prolonged period of time. Using probe ultrasonication and vortex to prepare IONPs suspensions of different particle sizes, the adsorption of arsenite and arsenate to bare hematite nanoparticles and hematite aggregates were investigated. To understand the difference in the adsorptive behavior, adsorption kinetics and isotherm parameters were determined. Both arsenite and arsenate were capable of adsorbing to hematite nanoparticles and hematite aggregates but the rate and capacity of adsorption is dependent upon the hematite particle size, the stability of the dispersion and the type of sorbed arsenic species. Once arsenic was adsorbed onto the hematite surface, both iron and arsenic can undergo redox transformation both microbially and photochemically and these processes can be intertwined. Arsenic speciation studies in the presence of hematite particles were performed and the effect of light on the redox process was preliminary quantified. The redox behavior of arsenite and arsenate were different depending on the hematite particle size, the stability of the suspension and the presence of environmental factors such as microbes and light. The results from this study are important and have significant environmental implications as arsenic mobility and bioavailability can be affected by its adsorption to hematite particles and by its surface mediated redox transformation. Moreover, this study furthers our understanding on how the particle size influences the interactions between IONPs and arsenic thereby clarifying the role of IONPs in the biogeochemical cycling of arsenic.^

Assessment of the occurrence and potential risks of pharmaceuticals and their metabolites in fish and water using liquid chromatography mass spectrometry

A comprehensive method for the analysis of 11 target pharmaceuticals representing multiple therapeutic classes was developed for biological tissues (fish) and water. Water samples were extracted using solid phase extraction (SPE), while fish tissue homogenates were extracted using accelerated solvent extraction (ASE) followed by mixed-mode cation exchange SPE cleanup and analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Among the 11 target pharmaceuticals analyzed, trimethoprim, caffeine, sulfamethoxazole, diphenhydramine, diltiazem, carbamazepine, erythromycin and fluoxetine were consistently detected in reclaimed water. On the other hand, caffeine, diphenhydramine and carbamazepine were consistently detected in fish and surface water samples. In order to understand the uptake and depuration of pharmaceuticals as well as bioconcentration factors (BCFs) under the worst-case conditions, mosquito fish were exposed to reclaimed water under static-renewal for 7 days, followed by a 14-day depuration phase in clean water. Characterization of the exposure media revealed the presence of 26 pharmaceuticals while 5 pharmaceuticals including caffeine, diphenhydramine, diltiazem, carbamazepine, and ibuprofen were present in the organisms as early as 5 h from the start of the exposure. Liquid chromatography ultra-high resolution Orbitrap mass spectrometry was explored as a tool to identify and quantify phase II pharmaceutical metabolites in reclaimed water. The resulting data confirmed the presence of acetyl-sulfamethoxazole and sulfamethoxazole glucuronide in reclaimed water. To my knowledge, this is the first known report of sulfamethoxazole glucuronide surviving intact through wastewater treatment plants and occurring in environmental water samples. Finally, five bioaccumulative pharmaceuticals including caffeine, carbamazepine, diltiazem, diphenhydramine and ibuprofen detected in reclaimed water were investigated regarding the acute and chronic risks to aquatic organisms. The results indicated a low potential risk of carbamazepine even under the worst case exposure scenario. Given the dilution factors that affect environmental releases, the risk of exposure to carbamazepine will be even more reduced.

Improved dynamic headspace sampling and detection using capillary microextraction of volatiles coupled to gas chromatography mass spectrometry

Sampling and preconcentration techniques play a critical role in headspace analysis in analytical chemistry. My dissertation presents a novel sampling design, capillary microextraction of volatiles (CMV), that improves the preconcentration of volatiles and semivolatiles in a headspace with high throughput, near quantitative analysis, high recovery and unambiguous identification of compounds when coupled to mass spectrometry. The CMV devices use sol-gel polydimethylsiloxane (PDMS) coated microglass fibers as the sampling/preconcentration sorbent when these fibers are stacked into open-ended capillary tubes. The design allows for dynamic headspace sampling by connecting the device to a hand-held vacuum pump. The inexpensive device can be fitted into a thermal desorption probe for thermal desorption of the extracted volatile compounds into a gas chromatography-mass spectrometer (GC-MS). The performance of the CMV devices was compared with two other existing preconcentration techniques, solid phase microextraction (SPME) and planar solid phase microextraction (PSPME). Compared to SPME fibers, the CMV devices have an improved surface area and phase volume of 5000 times and 80 times, respectively. One (1) minute dynamic CMV air sampling resulted in similar performance as a 30 min static extraction using a SPME fiber. The PSPME devices have been fashioned to easily interface with ion mobility spectrometers (IMS) for explosives or drugs detection. The CMV devices are shown to offer dynamic sampling and can now be coupled to COTS GC-MS instruments. Several compound classes representing explosives have been analyzed with minimum breakthrough even after a 60 min. sampling time. The extracted volatile compounds were retained in the CMV devices when preserved in aluminum foils after sampling. Finally, the CMV sampling device were used for several different headspace profiling applications which involved sampling a shipping facility, six illicit drugs, seven military explosives and eighteen different bacteria strains. Successful detection of the target analytes at ng levels of the target signature volatile compounds in these applications suggests that the CMV devices can provide high throughput qualitative and quantitative analysis with high recovery and unambiguous identification of analytes.

Elemental analysis and forensic comparison of soils by laser-induced breakdown spectroscopy (LIBS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS)

The elemental analysis of soil is useful in forensic and environmental sciences. Methods were developed and optimized for two laser-based multi-element analysis techniques: laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser-induced breakdown spectroscopy (LIBS). This work represents the first use of a 266 nm laser for forensic soil analysis by LIBS. Sample preparation methods were developed and optimized for a variety of sample types, including pellets for large bulk soil specimens (470 mg) and sediment-laden filters (47 mg), and tape-mounting for small transfer evidence specimens (10 mg). Analytical performance for sediment filter pellets and tape-mounted soils was similar to that achieved with bulk pellets. An inter-laboratory comparison exercise was designed to evaluate the performance of the LA-ICP-MS and LIBS methods, as well as for micro X-ray fluorescence (μXRF), across multiple laboratories. Limits of detection (LODs) were 0.01-23 ppm for LA-ICP-MS, 0.25-574 ppm for LIBS, 16-4400 ppm for μXRF, and well below the levels normally seen in soils. Good intra-laboratory precision (≤ 6 % relative standard deviation (RSD) for LA-ICP-MS; ≤ 8 % for μXRF; ≤ 17 % for LIBS) and inter-laboratory precision (≤ 19 % for LA-ICP-MS; ≤ 25 % for μXRF) were achieved for most elements, which is encouraging for a first inter-laboratory exercise. While LIBS generally has higher LODs and RSDs than LA-ICP-MS, both were capable of generating good quality multi-element data sufficient for discrimination purposes. Multivariate methods using principal components analysis (PCA) and linear discriminant analysis (LDA) were developed for discriminations of soils from different sources. Specimens from different sites that were indistinguishable by color alone were discriminated by elemental analysis. Correct classification rates of 94.5 % or better were achieved in a simulated forensic discrimination of three similar sites for both LIBS and LA-ICP-MS. Results for tape-mounted specimens were nearly identical to those achieved with pellets. Methods were tested on soils from USA, Canada and Tanzania. Within-site heterogeneity was site-specific. Elemental differences were greatest for specimens separated by large distances, even within the same lithology. Elemental profiles can be used to discriminate soils from different locations and narrow down locations even when mineralogy is similar.

Rapid inline derivatization of primary and secondary amine containing drugs by capillary electrophoresis with laser-induced fluorescence

Despite the ongoing "war on drugs" the seizure rates for phenethylamines and their analogues have been steadily increasing over the years. The illicit manufacture of these compounds has become big business all over the world making it all the more attractive to the inexperienced "cook". However, as a result, the samples produced are more susceptible to contamination with reactionary byproducts and leftover reagents. These impurities are useful in the analysis of seized drugs as their identities can help to determine the synthetic pathway used to make these drugs and thus, the provenance of these analytes. In the present work two fluorescent dyes, 4-fluoro-7-nitrobenzofurazan and 5-(4,6-dichlorotriazinyl)aminofluorescein, were used to label several phenethylamine analogues for electrophoretic separation with laser-induced fluorescence detection. The large scale to which law enforcement is encountering these compounds has the potential to create a tremendous backlog. In order to combat this, a rapid, sensitive method capable of full automation is required. Through the utilization of the inline derivatization method developed whereby analytes are labeled within the capillary efficiently in a minimum span of time, this can be achieved. The derivatization and separation parameters were optimized on the basis of a variety of experimentally determined factors in order to give highly resolved peaks in the fluorescence spectrum with limits of detection in the low µg/mL range.

Evaluation of non-contact sampling and detection of explosives using receiver operating characteristic curves

The growing need for fast sampling of explosives in high throughput areas has increased the demand for improved technology for the trace detection of illicit compounds. Detection of the volatiles associated with the presence of the illicit compounds offer a different approach for sensitive trace detection of these compounds without increasing the false positive alarm rate. This study evaluated the performance of non-contact sampling and detection systems using statistical analysis through the construction of Receiver Operating Characteristic (ROC) curves in real-world scenarios for the detection of volatiles in the headspace of smokeless powder, used as the model system for generalizing explosives detection. A novel sorbent coated disk coined planar solid phase microextraction (PSPME) was previously used for rapid, non-contact sampling of the headspace containers. The limits of detection for the PSPME coupled to IMS detection was determined to be 0.5-24 ng for vapor sampling of volatile chemical compounds associated with illicit compounds and demonstrated an extraction efficiency of three times greater than other commercially available substrates, retaining >50% of the analyte after 30 minutes sampling of an analyte spike in comparison to a non-detect for the unmodified filters. Both static and dynamic PSPME sampling was used coupled with two ion mobility spectrometer (IMS) detection systems in which 10-500 mg quantities of smokeless powders were detected within 5-10 minutes of static sampling and 1 minute of dynamic sampling time in 1-45 L closed systems, resulting in faster sampling and analysis times in comparison to conventional solid phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) analysis. Similar real-world scenarios were sampled in low and high clutter environments with zero false positive rates. Excellent PSPME-IMS detection of the volatile analytes were visualized from the ROC curves, resulting with areas under the curves (AUC) of 0.85-1.0 and 0.81-1.0 for portable and bench-top IMS systems, respectively. Construction of ROC curves were also developed for SPME-GC-MS resulting with AUC of 0.95-1.0, comparable with PSPME-IMS detection. The PSPME-IMS technique provides less false positive results for non-contact vapor sampling, cutting the cost and providing an effective sampling and detection needed in high-throughput scenarios, resulting in similar performance in comparison to well-established techniques with the added advantage of fast detection in the field.

Structural flexibility and oxygen diffusion pathways in monomeric fluorescent proteins

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

Speciation, metabolism, toxicity, and protein-binding of different arsenic species in human cells

Despite of its known toxicity and potential to cause cancer, arsenic has been proven to be a very important tool for the treatment of various refractory neoplasms. One of the promising arsenic-containing chemotherapeutic agents in clinical trials is Darinaparsin (dimethylarsinous glutathione, DMA III(GS)). In order to understand its toxicity and therapeutic efficacy, the metabolism of Darinaparsin in human cancer cells was evaluated. With the aim of detecting all potential intermediates and final products of the biotransformation of Darinaparsin and other arsenicals, an analytical method employing high performance liquid chromatography inductively coupled mass spectrometry (HPLC-ICP-MS) was developed. This method was shown to be capable of separating and detecting fourteen human arsenic metabolites in one chromatographic run. The developed analytical technique was used to evaluate the metabolism of Darinaparsin in human cancer cells. The major metabolites of Darinaparsin were identified as dimethylarsinic acid (DMAV), DMA III(GS), and dimethylarsinothioyl glutathione (DMMTAV(GS)). Moreover, the method was employed to study the conditions and mechanisms of formation of thiol-containing arsenic metabolites from DMAIII(GS) and DMAV as the mechanisms of formation of these important As species were unknown. The arsenic sulfur compounds studied included but were not limited to the newly discovered human arsenic metabolite DMMTA V(GS) and the unusually highly toxic dimethylmonothioarsinic acid (DMMTAV). It was found that these species may form from hydrogen sulfide produced in enzymatic reactions or by utilizing the sulfur present in protein persulfides. Possible pathways of thiolated arsenical formation were proposed and supporting data for their existence provided. In addition to known mechanism of arsenic toxicity such as protein-binding and reactive oxygen formation, it was proposed that the utilization of thiols from protein persulfides during the formation of thiolated arsenicals may be an additional mechanism of toxicity. The toxicities of DMAV(GS), DMMTA V, and DMMTAV(GS) were evaluated in cancer cells, and the ability of these cells to take the compounds up were compared. When assessing the toxicity by exposing multiple myeloma cells to arsenicals externally, DMMTAV(GS) was much less toxic than DMAIII(GS) and DMMTAV, probably as a result of its very limited uptake (less than 10% and 16% of DMAIII(GS) and DMMTAV respectively).^

Covalent protein adduction of nitrogen mustards and related compounds

Chemical warfare agents continue to pose a global threat despite the efforts of the international community to prohibit their use in warfare. For this reason, improvement in the detection of these compounds remains of forensic interest. Protein adducts formed by the covalent modification of an electrophilic xenobiotic and a nucleophilic amino acid may provide a biomarker of exposure that is stable and specific to compounds of interest (such as chemical warfare agents), and have the capability to extend the window of detection further than the parent compound or circulating metabolites. This research investigated the formation of protein adducts of the nitrogen mustard chemical warfare agents mechlorethamine (HN-2) and tris(2-chloroethyl)amine (HN-3) to lysine and histidine residues found on the blood proteins hemoglobin and human serum albumin. Identified adducts were assessed for reproducibility and stability both in model peptide and whole protein assays. Specificity of these identified adducts was assessed using in vitro assays to metabolize common therapeutic drugs containing nitrogen mustard moieties. Results of the model peptide assays demonstrated that HN-2 and HN-3 were able to form stable adducts with lysine and histidine residues under physiological conditions. Results for whole protein assays identified three histidine adducts on hemoglobin, and three adducts (two lysine residues and one histidine residue) on human serum albumin that were previously unknown. These protein adducts were determined to be reproducible and stable at physiological conditions over a three-week analysis period. Results from the in vitro metabolic assays revealed that adducts formed by HN-2 and HN-3 are specific to these agents, as metabolized therapeutic drugs (chlorambucil, cyclophosphamide, and melphalan) did not form the same adducts on lysine or histidine residues as the previously identified adducts formed by HN-2 and HN-3. Results obtained from the model peptide and full protein work were enhanced by comparing experimental data to theoretical calculations for adduct formation, providing further confirmatory data. This project was successful in identifying and characterizing biomarkers of exposure to HN-2 and HN-3 that are specific and stable and which have the potential to be used for the forensic determination of exposure to these dangerous agents.

The Creation and Evaluation of Novel Canine Training Aids for Cocaine Using Molecularly Encapsulated Sol-Gel Polymers and an Investigation of Canine Field Accuracy

Biological detectors, such as canines, are valuable tools used for the rapid identification of illicit materials. However, recent increased scrutiny over the reliability, field accuracy, and the capabilities of each detection canine is currently being evaluated in the legal system. For example, the Supreme Court case, State of Florida v. Harris, discussed the need for continuous monitoring of canine abilities, thresholds, and search capabilities. As a result, the fallibility of canines for detection was brought to light, as well as a need for further research and understanding of canine detection. This study is two-fold, as it looks to not only create new training aids for canines that can be manipulated for dissipation control, but also investigates canine field accuracy to objects with similar odors to illicit materials. It was the goal of this research to improve upon current canine training aid mimics. Sol-gel polymer training aids, imprinted with the active odor of cocaine, were developed. This novel training aid improved upon the longevity of currently existing training aids, while also provided a way to manipulate the polymer network to alter the dissipation rate of the imprinted active odors. The manipulation of the polymer network could allow handlers to control the abundance of odors presented to their canines, familiarizing themselves to their canine’s capabilities and thresholds, thereby increasing the canines’ strength in court. The field accuracy of detection canines was recently called into question during the Supreme Court case, State of Florida v. Jardines, where it was argued that if cocaine’s active odor, methyl benzoate, was found to be produced by the popular landscaping flower, snapdragons, canines will false alert to said flowers. Therefore, snapdragon flowers were grown and tested both in the laboratory and in the field to determine the odors produced by snapdragon flowers; the persistence of these odors once flowers have been cut; and whether detection canines will alert to both growing and cut flowers during a blind search scenario. Results revealed that although methyl benzoate is produced by snapdragon flowers, certified narcotics detection canines can distinguish cocaine’s odor profile from that of snapdragon flowers and will not alert.

Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Development of a Lab-on-a-Chip Device for Rapid Nanotoxicity Assessment In Vitro

Increasing useof nanomaterials in consumer products and biomedical applications creates the possibilities of intentional/unintentional exposure to humans and the environment. Beyond the physiological limit, the nanomaterialexposure to humans can induce toxicity. It is difficult to define toxicity of nanoparticles on humans as it varies by nanomaterialcomposition, size, surface properties and the target organ/cell line. Traditional tests for nanomaterialtoxicity assessment are mostly based on bulk-colorimetric assays. In many studies, nanomaterials have found to interfere with assay-dye to produce false results and usually require several hours or days to collect results. Therefore, there is a clear need for alternative tools that can provide accurate, rapid, and sensitive measure of initial nanomaterialscreening. Recent advancement in single cell studies has suggested discovering cell properties not found earlier in traditional bulk assays. A complex phenomenon, like nanotoxicity, may become clearer when studied at the single cell level, including with small colonies of cells. Advances in lab-on-a-chip techniques have played a significant role in drug discoveries and biosensor applications, however, rarely explored for nanomaterialtoxicity assessment. We presented such cell-integrated chip-based approach that provided quantitative and rapid response of cellhealth, through electrochemical measurements. Moreover, the novel design of the device presented in this study was capable of capturing and analyzing the cells at a single cell and small cell-population level. We examined the change in exocytosis (i.e. neurotransmitterrelease) properties of a single PC12 cell, when exposed to CuOand TiO2 nanoparticles. We found both nanomaterials to interfere with the cell exocytosis function. We also studied the whole-cell response of a single-cell and a small cell-population simultaneously in real-time for the first time. The presented study can be a reference to the future research in the direction of nanotoxicity assessment to develop miniature, simple, and cost-effective tool for fast, quantitative measurements at high throughput level. The designed lab-on-a-chip device and measurement techniques utilized in the present work can be applied for the assessment of othernanoparticles' toxicity, as well.