Novel Low Dimensional Sensors for Rapid Disease Diagnosis and Efficient Biomolecular Detection

Nanomaterials have been used in diverse biosensing applications over the years for their unique properties compared to their ‘bulk’ counterparts. The quantum effects observed in nanomaterials of different dimensions have been exploited, in particular, for fluorescence sensing using surface plasmons. The present work is directed towards the understanding of these effects and the physics behind such plasmons and its application. In the first chapter (Chapter 1), a succinct introduction to quantum confinement and fluorescence biosensors has been presented, followed by a brief overview of the applications of nanomaterials in biosensing. Chapter 2 focuses on the various analytical and characterization techniques used in this work. Chapter 3 describes the effects of shape on the plasmonic enhancement in silver nanoparticles. In chapter 4, the work on the development of a novel bio-sensing platform (AIDLuQ) has been outlined along with its use in the ultrasensitive detection of biomolecules. Building on chapter 4, the AIDLuQ platform was used for a real-life application in the detection of a cancer biomarker. This was supported with DFT simulations providing an insight into the electronic interactions between graphene and the quantum dots at the nano-scale. This has been described in chapter 5. These findings lay the groundwork for further in-depth research to study the linear as well as non-linear optical interactions in nanoparticles in the vicinity of other nanoparticles, as elucidated in chapter 6

Methanobactin: Metal binding properties, physiological function and biosynthesis

Methanobactins (mbs) are low molecular mass (\u3c 1300 Da) modified peptides secreted by many methanotrophs or methane oxidizing bacteria to sequester copper from the environment. To date, methanobactin has been structurally characterized from six methanotrophs and can be divided into two groups. Group I methanobactins are represented by methanobactins from Methylosinus trichosporium OB3b and Methylosinus sp. LW4. This group is characterized by the presence of two oxazolone rings with adjacent thioamide groups. Two nitrogens from the oxazolone rings and two sulfurs from the thioamide groups come together to form a copper coordination site in distorted tertrahedral geometry. This group of methanobactin also has two cysteines in the mature protein that form a stable disulfide bond. The second group is composed of methanobactins from four different Methylocystis species. This group of methanobactins has a hairpin like structure following copper binding with sulfate group attached to serine or threonine and is structurally more dynamic than group I methanobactins. This group is also characterized by the presence of a C-terminal oxazolone ring with an associated thioamide and either an N-terminal imidazolone or pyrazinedione group and an associated thioamide. The first part of this dissertation is focused on the study of methanobactin binding to various non-copper metals such as mercury and gold and the role of that binding of noncopper metals has on the physiology of methanotrophs. The second part of this dissertation is focused on understanding the post-translational modifications required for methanobactin. Until recently, the biosynthesis was assumed to be via a non-ribosomal peptide synthase or polyketide synthase. However, during the course of my dissertation, we determined that methanobactin is indeed produced ribosomally and post-translationally modified. I show in this dissertation that TonB-dependent transporter gene in the methanobactin gene cluster is involved in the uptake of copper-bound methanobactin. In addition, we demonstrate that mbnN is involved in the deamination of the N-terminal oxazolone ring, a post-translational modification required in the formation of the N-terminal oxazolone ring in the methanobactin from Methylosinus trichosporium OB3b. The results and methods used in this research would further help determine the role of other genes involved in biosynthesis of methanobactin and bioengineer methanobactin for various human and animal health purposes. In light of recent evidence of methanobactin being effective chelator of excess copper in Wilson’s disease in rat models, understanding the biosynthesis of methanobactin has become more important

Ultrasensitive Immunosensing Platform Based on Analyte Induced Disruption of Luminescence Quenching (AIDLuQ)

In this study, we design an extremely fast and sensitive immunosensing platform using graphene as the sensing platform. A solution containing a mixture of graphene nanoplatelets and gold nanoparticles was coated on to a copier paper using a spray gun to form a uniform coating. Fluorescent quantum dots (QDs) functionalized with antibodies (Ab) were drop casted on to this platform, whose fluorescence was quenched by the graphene on the graphene/gold paper. With the addition of the antigen to this graphene/gold-QD-Ab complex, a disruption of quenching was observed, and the fluorescence intensity increased with increasing concentration of the antigen. A detection limit of as low as 10 fM was obtained for the detection of human Immunoglobulin G (IgG)

PNEUMOCOCCAL BIOFILMS AND THEIR INTERVENTION STRATEGIES

Pneumonia is a fatal infection with hard time breathing, cough, and fever. The children are at high risk worldwide due to pneumonia. This is responsible for childhood mortality and morbidity worldwide. It is mainly caused by bacteria. Pneumonia-causing bacteria are resistant to most of the antibiotics and therapeutic agents due to the formation of biofilms. Laboratories around the world are trying to develop strategies to combat pneumococcal biofilms. This review deals with the formation of pneumococcal biofilms and their different intervention strategies.Â

Study of cyclic bursting loading on needle-punched nonwovens: Part II – Change in air permeability and compression behavior

Efforts have been made to investigate the physical properties of needle-punched nonwovens, such as compression and air permeability, before and after the application of cyclic bursting pressure. It is observed that the structural parameters, such as areal density, needling density and fibre fineness, have significant effect on the aforementioned fabric characteristics. More compression is observed in a sample with low mass density. Sample made of coarser fibre shows lower compression as compared to finer fibre samples. The air permeability decreases with increase in mass density. On conducting cyclic bursting test on a sample, the values of air permeability and compression change significantly. The cyclic parameters, such as pressure magnitude and rest time at cyclic peak pressure, cause significant structural changes and reorientation of the fibre during deformation. Increase in pressure and rest time causes increase in compression parameter (α) and air permeability. Nevertheless, at low cyclic pressure level (10% of bursting pressure), the network becomes compact due to fibrous reorientation, and therefore both the values of compression parameter (α) and air permeability show initial drop. On examining the samples made of coarser and finer fibres, the variation is observed in the extent of change in the air permeability

Cyclic bursting loading on needle-punched nonwovens: Part I – Distention behavior

The present study aims at examining different needle-punched polypropylene nonwovens under different cyclic bursting pressure. Various fabric parameters including mass density, punch density and fibre fineness have been investigated. For the cyclic test, the distension is measured at different cyclic bursting pressures proportionate to the bursting strength of the fabric. Other parameters including the cyclic pressure magnitude, the number of cycles, and the rest time at peak pressure have also been investigated. It has been found that the bursting strength and distension of fabric increase with an increase in mass density, while they show opposite trend with punch density and fibre denier (p < 0.01). The distension value of each sample increases with an increase in the cyclic parameters i.e. number of loading cycle, rest time and pressure peak

Partial Pressure Assisted Growth of Single-Layer Graphene Grown by Low-Pressure Chemical Vapor Deposition: Implications for High-Performance Graphene FET Devices

An attempt has been made to understand the thermodynamic mechanism study of the low-pressure chemical vapor deposition (LPCVD) process during single-layer graphene (SLG) growth as it is the most debatable part of the CVD process. The intensive studies are being carried out worldwide to enhance the quality of LPCVD-grown graphene up to the level of mechanically exfoliated SLG. The mechanism and processes have been discussed earlier by several research groups during the variation in different parameters. However, the optimization and mechanism involvement due to individual partial pressure-based effects has not been elaborately discussed so far. Hence, we have addressed this issue in detail including thermodynamics of the growth process and tried to establish the effect of the partial pressures of individual gases during the growth of SLG. Also, optical microscopy, Raman spectroscopy, and atomic force microscopy (AFM) have been performed to determine the quality of SLG. Furthermore, nucleation density has also been estimated to understand a plausible mechanism of graphene growth based on partial pressure. Moreover, the field-effect transistor (FET) device has been fabricated to determine the electrical properties of SLG, and the estimated mobility has been found as similar to 2595 cm(2) V-1 s(-1) at n = -2 x 10(12) cm(-2). Hence, the obtained results trigger that the partial pressure is an important parameter for the growth of SLG and having various potential applications in high-performance graphene FET (GFET) devices

An Exemplar for Teaching and Learning Qualitative Research

In this article, we outline a course wherein the instructors teach students how to conduct rigorous qualitative research. We discuss the four major distinct, but overlapping, phases of the course: conceptual/theoretical, technical, applied, and emergent scholar. Students write several qualitative reports, called qualitative notebooks, which involve data that they collect (via three different types of interviews), analyze (using nine qualitative analysis techniques via qualitative software), and interpret. Each notebook is edited by the instructors to help them improve the quality of subsequent notebook reports. Finally, we advocate asking students who have previously taken this course to team-teach future courses. We hope that our exemplar for teaching and learning qualitative research will be useful for teachers and students alike

Effect of post–emergence application of cyhalofop-butyl for weed management in direct-seeded rice (Oryza sativa)

A field experiment was conducted during rainy season of 2009 at the research farm of the Indian Agricultural Research Institute, New Delhi to evaluate the appropriate combination of pre-emergence and post-emergence herbicides in direct-seeded rice (Oryza sativa L.). All the weed control treatments brought significant increase in grain (25-52%) and straw yield (27-58%) as compared to season long crop weed competition. Cyhalofop-butyl residues in soil were found below detectable level indicating safety to soil microbial population and succeeding crop. It may be concluded that weeds can be managed during critical period of competition with the sequential application of pretilachlor (750 g/ha) as pre-emergence followed by post- emergence application of cyhalofop-butyl (60 g/ha) at 30 DAS in direct-seeded rice

Post-Transplant Outcomes in High-Risk Compared with Non-High-Risk Multiple Myeloma: A CIBMTR Analysis.

Conventional cytogenetics and interphase fluorescence in situ hybridization (FISH) identify high-risk multiple myeloma (HRM) populations characterized by poor outcomes. We analyzed these differences among HRM versus non-HRM populations after upfront autologous hematopoietic cell transplantation (autoHCT). Between 2008 and 2012, 715 patients with multiple myeloma identified by FISH and/or cytogenetic data with upfront autoHCT were identified in the Center for International Blood and Marrow Transplant Research database. HRM was defined as del17p, t(4;14), t(14;16), hypodiploidy (-Y) or chromosome 1 p and 1q abnormalities; all others were non-HRM. Among 125 HRM patients (17.5%), induction with bortezomib and immunomodulatory agents (imids) was higher compared with non-HRM (56% versus 43%, P \u3c .001) with similar pretransplant complete response (CR) rates (14% versus 16%, P .1). At day 100 post-transplant, at least a very good partial response was 59% in HRM and 61% in non-HRM (P = .6). More HRM patients received post-transplant therapy with bortezomib and imids (26% versus 12%, P = .004). Three-year post-transplant progression-free (PFS) and overall survival (OS) rates in HRM versus non-HRM were 37% versus 49% (P \u3c .001) and 72% versus 85% (P \u3c .001), respectively. At 3 years, PFS for HRM patients with and without post-transplant therapy was 46% (95% confidence interval [CI], 33 to 59) versus 14% (95% CI, 4 to 29) and in non-HRM patients with and without post-transplant therapy 55% (95% CI, 49 to 62) versus 39% (95% CI, 32 to 47); rates of OS for HRM patients with and without post-transplant therapy were 81% (95% CI, 70 to 90) versus 48% (95% CI, 30 to 65) compared with 88% (95% CI, 84 to 92) and 79% (95% CI, 73 to 85) in non-HRM patients with and without post-transplant therapy, respectively. Among patients receiving post-transplant therapy, there was no difference in OS between HRM and non-HRM (P = .08). In addition to HRM, higher stage, less than a CR pretransplant, lack of post-transplant therapy, and African American race were associated with worse OS. In conclusion, we show HRM patients achieve similar day 100 post-transplant responses compared with non-HRM patients, but these responses are not sustained. Post-transplant therapy appeared to improve the poor outcomes of HRM