Doctor of Philosophy

dissertationCurrently, all over the world, a lot of money is being pumped into the healthcare domain to facilitate development of rapid, point-of-care disease diagnostic platforms, which are relatively cheap with enhanced ease-of-use capabilities that can be deployed in low-resource settings which have higher prevalence of disease infected cases. Volatile organic compounds (VOCs) represent one class of biomarkers that has been less explored but possesses immense potential from a disease diagnostic standpoint. Tuberculosis (TB) has been a cause of significant health concern affecting a large population of people in Africa and Asia and recently, researchers have identified four specific TB VOCs from the breath of infected patients, through GC-MS analysis techniques. Rapid, accurate diagnosis is critical for timely initiation of treatment and, ultimately, control of the disease. Lack of access to appropriate diagnostic tools is caused, in part, by shortcomings as currently available diagnostics are often ill-adapted to resource-limited settings or specific patient needs, or may be priced out of reach. Although many countries still rely on basic tools such as smear microscopy, new diagnostics are changing the TB diagnostics landscape. Some groups have previously attempted to develop breath-based TB detection techniques utilizing evanescent wave technology and colorimetry-based pattern detection techniques, but no sensors exist for detection of the four methyl ester-based VOCs. In the research presented in this dissertation, we have attempted to develop a low-cost, metal functionalized titania nanotubular array-based sensor platform for electrochemical detection of the four major TB volatile organic biomarkers (VOBs). TiO2 or titania nanotubes is an easy-to-synthesize, robust, wide bandgap (~3.2 eV) semiconductor material with excellent vectorial charge transport properties. In addition, the nanotubular morphology presents a large surface-area-to-volume ratio with sufficient metal bound active sites which facilitates efficient binding with the VOBs of interest. Titania nanotubes with an optimized morphology and stoichiometry and functionalized with cobalt through the incipient wetting impregnation, and an in-situ lattice functionalization method for electrochemical detection of the four TB VOBs and their subsequent integration into a sensor hardware, has been investigated. The potential light assisted, plasmonic-based sensing capabilities of gold nanoparticle functionalized TiO2 nanotubes have been illustrated as well. In the end, a similar but slightly tweaked sensing platform has been tested for the detection of nonpulmonary colorectal cancer as well, extending the detection capabilities of the fabricated sensor substrate and leaving room for further research for screening of other life-threatening diseases. Improved access to better TB screening and diagnostics may present potential opportunities that may include efforts to accelerate market entry and/or scale-up of the innovative sensing platform that addresses unmet needs

Master of Science

thesisThe industrial use of activated carbon for gold adsorption from alkaline cyanide leach solutions has been a major development in gold hydrometallurgy which was commercialized during the last part of the 20th century. In the gold industry, activated carbon is most often used to adsorb gold from dilute alkaline cyanide solutions. The gold is dissolved as the Au(CN)2 - complex and is recovered from the solution by Carbon-in- Pulp (CIP) or Carbon-in-Leach (CIL) processes. Activated carbon loaded with gold must be treated by an elution step to desorb the gold for subsequent recovery. In this way, a smaller volume of higher grade gold solution is produced, suitable for final gold recovery by electrowinning. The gold elution efficiency can be increased by the use of hydro-alcoholic solution and high temperature. The effect of particle size on gold elution has not been studied. In this regard, experiments have been performed with different size fractions of activated carbon to study the stripping characteristics of activated carbon for gold elution. It has been observed that it is difficult to elute gold from fine activated carbon which is quite contrary to fundamental expectations. From a technological point of view, it is necessary to develop improved methods of stripping for enhanced gold recovery from alkaline cyanide solutions. As part of this work, to overcome the problem of gold elution from fine carbon, alternative elution procedures have been developed and discussed. These include, use of hydro-alcoholic solutions, use of vacuum degassing prior to stripping, and application of external pressure. Research on this topic is carried out to enhance the understanding of the science involved in the elution of gold from fine activated carbon. Hence, current research focuses on finding a plausible explanation to explain the difficulty of eluting gold from fine activated carbon. The emphasis of this research is to address the stripping by experimentation and with the aid of computational chemistry tools. Since activated carbon consists of a cryptocrystalline graphitic structure which contributes significantly to gold adsorption, research on HOPG (highly oriented pyrolytic graphite) is in progress to determine the nature of graphite surfaces, their wetting characteristics, and their significance in gold adsorption / desorption from alkaline cyanide solutions. Computational chemistry analysis of adsorbed aurodicyanide anions at graphite surfaces are being done to understand the nature of gold adsorption/desorption from alkaline cyanide solutions by activated carbon. Current results from these surface chemistry studies are used to discuss the state of gold cyanide at activated carbon surfaces and the anomalous elution dependence on particle size

The CERN disposal of the FELIX project proposal: Some comments on and justification for it

The authors seriously questioned and still continue to question the overemphasised “prospects” in the past of the so-called FELIX project in the domain of ultrahigh-energy astroparticle physics and the optimism that was nourtured around it. This was and is somewhat irrational because there is so far no dearth in the accumulated data for the testing of the models for particle production. But that up to now we failed to build up a really and concretely standard theory of particle production is due to our poverty in outllook and philosophy. The authors picked up and pointed out the very basic down-to-earth observables which even in the available energy range would really suffice to judge the merits and successes of any of the models. That the spirit of FELIX-like proposals might resurrect with just some other name even after the present (and temporary?) setback of the FELIX project remains the point of concern to the authors

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Assessment by Ames test and comet assay of toxicity potential of polymer used to develop field-capable rapid-detection device to analyze environmental samples

There is need for devices that decrease detection time of food-borne pathogens from days to real-time. In this study, a rapid-detection device is being developed and assessed for potential cytotoxicity. The device is comprised of melt-spun polypropylene coupons coated via oxidative chemical vapor deposition (oCVD) with 3,4-Ethylenedioxythiophene (EDOT), for conductivity and 3-Thiopheneethanol (3TE), allowing antibody attachment. The Ames test and comet assay have been used in this study to examine the toxicity potentials of EDOT, 3TE, and polymerized EDOT-co-3TE. For this study, Salmonella typhimurium strain TA1535 was used to assess the mutagenic potential of EDOT, 3TE and the copolymer. The average mutagenic potential of EDOT, 3TE and copolymer was calculated to be 0.86, 0.56, and 0.92, respectively. For mutagenic potential, on a scale from 0 to 1, close to 1 indicates low potential for toxicity, whereas a value of 0 indicates a high potential for toxicity. The comet assay is a single-cell gel electrophoresis technique that is widely used for this purpose. This assay measures toxicity based on the area or intensity of the comet-like shape that DNA fragments produce when DNA damage has occurred. Three cell lines were assessed; FRhK-4, BHK-21, and Vero cells. After averaging the results of all three strains, the tail intensity of the copolymer was 8.8 % and tail moment was 3.0, and is most similar to the untreated control, with average tail intensity of 5.7 % and tail moment of 1.7. The assays conducted in this study provide evidence that the copolymer is non-toxic to humans. Keywords: Biosensor; Cytotoxicity; oCVD; P(EDOT-co-3TE

Detection of Four Distinct Volatile Indicators of Colorectal Cancer using Functionalized Titania Nanotubular Arrays

Screening of colorectal cancer is crucial for early stage diagnosis and treatment. Detection of volatile organic compounds (VOCs) of the metabolome present in exhaled breath is a promising approach to screen colorectal cancer (CRC). Various forms of volatile organic compounds (VOCs) that show the definitive signature for the different diseases including cancers are present in exhale breathe. Among all the reported CRC VOCs, cyclohexane, methylcyclohexane, 1,3-dimethyl- benzene and decanal are identified as the prominent ones that can be used as the signature for CRC screening. In the present investigation, detection of the four prominent VOCs related to CRC is explored using functionalized titania nanotubular arrays (TNAs)-based sensor. These signature biomarkers are shown to be detected using nickel-functionalized TNA as an electrochemical sensor. The sensing mechanism is based on the electrochemical interaction of nickel-functionalized nanotubes with signature biomarkers. A detailed mechanism of the sensor response is also presented