<p> Popular theories about the origin of life can be classified to two classes: metabolism first or genes first. As a metabolism first theory, the lipid world theory, in which non-covalent assemblies of lipids, such as micelles and vesicles store information in the form of a non-random molecular composition, has been proposed to investigate the possibility of inheritance without genes. Our models assume that interaction occurs between nearest neighbour molecules only, and account for spatial segregation of molecules of different types within the assembly. We also draw a distinction between a self-assembly model, in which the composition is determined by mutually favourable interaction energies between the molecules, and a catalytic model, in which the composition is determined by mutually favourable catalysis. We show that compositional inheritance occurs in both models, although the self-assembly case seems more relevant if the molecules are simple lipids. In the case where the assemblies are composed of just two types of molecules, there is a strong analogy with the classic two-allele Moran model from population genetics. This highlights the parallel between compositional inheritance and genetic inheritance. We also investigated the polymerization reactions which may bridge the gap between simple organic molecules and the beginning of the RNA world, which belongs to the class of genes first theories. We found that different from normal chemical systems, catalysts for the polymerization system can shift the equilibrium toward longer polymers. Together with RNA's potential as catalyst, the RNA polymerization system may form a feedback loop which makes the formation of functional RNA molecules easier, and come more close to the beginning of RNA world.</p> / Thesis / Master of Science (MSc)

In the post-genomic era, one of the most important goals for the community of plant biologists is to take full advantage of the knowledge generated by the Arabidopsis thaliana genome project, and to employ state-of-the-art functional genomics techniques to assign function to each gene. This will be achieved through a complete understanding of what all cellular components do, and how they interact with one another to produce a phenotype. Among the proteins encoded by the Arabidopsis genome are 24 related carboxyl methyltransferases that belong to the SABATH family. Several of the SABATH methyltransferases convert plant hormones, like jasmonic acid, indole-3-acetic acid, salicylic acid, gibberellins, and other plant constituents into methyl esters, thereby regulating the biological activity of these molecules and, consequently, myriad important physiological processes. Our research aims to decipher the function of proteins belonging to the SABATH family by applying a combination of genomics tools, including genome-wide expression analysis and gas-chromatography coupled with mass spectrometry-based metabolite profiling. Our results, combined with available biochemical information, provide a better understanding of the physiological role of SABATH methyltransferases, further insights into secondary plant metabolism and deeper knowledge of the consequences of modulating the expression of SABATH methyltransferases, both at the genome-wide expression and metabolite levels. / Ph. D.

Size Exclusion Chromatography (SEC) is a liquid chromarographic technique used for the characterization of polymers and polymer related materials and also for the separation of small molecules. The major drawback of SEC is the lack of availability of a universal and true mass detector for providing a homogeneous response for all samples. Indirect detection methods have demonstrated to supply an alternative way to obtain a universal, sensitive and mass response in liquid chromatography. This research evaluated the indirect conductivity detection method for the size exclusion chromatographic separation of small molecules. Several studies were developed in order to understand the performance of this novel indirect detection mode. The evaluation of the initial experimental conditions snowed a dependence on the response, efficiency and elution time with the concentration of the conductivity probe added to the mobile phase. The SEC calibration curves developed for a series of standards indicated that selected conditions do not affect the separation by size. Response factors revealed a slight increase with molecular weight when they are expressed in volume or mass. Limits of detection were in the order of 20 nanoliters for small molecules. The effect of different conductivity probes on the separation and response was also studied. A modification of the original detector cell design resulted in improvement in the signal to noise ratio. / Master of Science

<p dir="ltr">This study has focused on the role of novel boronic acid (BA) and nicotinamide-ponatinib analogs to address current limitations in the treatment of difficult-to-treat cancers including renal, breast and lung cancer. As is well-known, CLK and ROCK have been implicated as oncogenic kinases across several cancer types. However, there are research gaps in the development of CLK/ROCKi. For instance, currently none of the CLKi have been FDA-approved. This study has identified novel BA-containing pyrazolo[4,3-<i>f</i>]quinoline scaffolds that are potent, dual CLK/ROCKi, which are highly active against the renal cancer cell line, Caki-1 based on the NCI screening data. Based on kinase and cancer cell line screening, the top compounds were identified and mechanistic studies indicated that the compounds promoted DNA damage in Caki-1. We also gained insight into the binding modes of the compounds via docking analysis. Furthermore, flow cytometry analysis indicated that the top compounds promote cell cycle arrest. Additionally, qPCR and western analysis indicated that the top compound, <b>HSD1791</b>, suppresses cyclinD/Rb pathway, thereby providing a mechanistic basis for cell cycle arrest. Concerning the challenges in the treatment of breast and lung cancer, it is known that despite advances in chemotherapy and immunotherapy, the survival rate of patients is poor at the advanced stage of the diseases. Oncogenic kinases such as p70S6K and MNK have been independently implicated in breast and lung tumorigenesis, however synergistically targeting MNK/p70S6K pathways using single agents remains a challenge. In this study, we have identified the novel lead candidate, <b>HSND80</b>, which is a potent dual MNK/p70S6Ki with remarkable activity against breast and non-small cell lung cancer cell lines. We identified the mechanism of tumor cell growth suppression using proteomics, immunoblotting, and cell cycle analysis. Moreover, <b>HSND80</b> has demonstrated tumor growth suppression effects <i>in vivo</i>. Additionally, pharmacokinetics, plasma protein binding, and hERG safety analysis indicated <b>HSND80</b> has suitable drug-like properties. Together, these findings indicate that it has promising functions as an anticancer therapeutic. In conclusion, this study has focused on identifying and characterizing novel pyrazolo[4,3-<i>f</i>]quinoline scaffolds and nicotinamide ponatinib analogs as promising tumor-agnostic therapeutics.</p>

Influenza A viruses (IAV) are negative sense RNA viruses that naturally infect a wide variety of animals. Different subtypes of the virus infect waterfowl, poultry, pigs, horses, ferrets, bats, dogs, cats and humans, causing zoonotic outbreaks and pandemics. In humans, IAV strains cause seasonal epidemics that can result in up to 50000 deaths and 700000 hospitalizations each year, and ranks in the top ten causes of death in the United States. In addition, virulent strains of IAV have caused pandemic outbreaks triggering numerous fatalities. While tropism to the upper respiratory tract is important for virus transmission, infection of the lower lung is most correlated with pathogenesis. The mammalian lung has multiple structural cell types, of which two classes are considered most important for IAV pathogenesis. These are (1) alveolar unit cells and (2) cells of the conducting airways, primarily those of the bronchi and bronchioles. Alveolar unit cells, or pneumocytes, chiefly comprise type I and type II alveolar epithelial cells, and are involved in gas exchange and surfactant production. Cells of the bronchi and bronchioles (e.g., basal, secretory, ciliated, club, goblet and neuroendocrine cells) perform numerous functions related to tissue repair/renewal, and mucous production. Upon IAV infection the regulated (or programmed) death of the infected cell represents an important pathogen clearance mechanism. Programmed cell death can be largely non-inflammatory (e.g., apoptosis) or pro-inflammatory (e.g., necroptosis). In this dissertation, I outline experiments carried out to identify the role of pro-inflammatory programmed cell death in influenza A virus clearance and pathogenesis both in vitro and in vivo. My work outlines the role of necroptosis in IAV clearance, and how this controlled form of cell death, particularly in alveolar unit cells, can be exploited as a potential new therapeutic avenue for severe influenza disease. / Cancer Biology & Genetics

No / Our objectives were to obtain monoclonal anti-endothelial cell antibodies (AECA) from systemic lupus erythematosus (SLE) patients, to characterize their antigen specificity, and their capability to induce a pro-inflammatory and pro-adhesive endothelial phenotype, and to investigate the mechanism of endothelial cell (EC) activation in vitro. Monoclonal IgG AECA were generated by hybridoma formation with human SLE B cells. Antigen specificity was characterized by immunoblotting with enriched cell membrane fractions, by cytofluorimetry and by cell solid-phase ELISA. Endothelial activation was evaluated by measuring increases in U937 cell adhesiveness, adhesion molecule (E-selectin and ICAM-1) expression and IL-6 production. In addition, mechanisms of endothelial activation were investigated by assessment of NF-B by measuring the loss of its inhibitor I-B. mAb E-3 bound live EC and recognized a 42 kDa EC membrane protein, it enhanced U937 adhesiveness, E-selectin and ICAM-1 expression and IL-6 production, and caused the loss of I-B. We conclude this is the first in vitro demonstration that a human monoclonal AECA from a SLE patient reacts with a constitutive endothelial membrane antigen and induces a pro-inflammatory endothelial phenotype through NF-B activation.

We study the nonlinear mean-field dynamics of diatomic molecule formation at coherent photo- and magneto-association of ultracold atoms focusing on the case when the system is initially in the all-atomic state. We show that in the limit of strongly nonlinear interaction between an ultra-cold atomic-molecular system and a quasi-resonant electromagnetic field, the molecule formation process, depending on the characteristics of the associating field, may evolve according two different scenarios, namely, weak- and strong-oscillatory regimes. In the first case the number of molecules increases without pronounced oscillations of atom-molecule populations, while in the second case high-amplitude Rabi-type oscillations arise. Assuming an arbitrary external field configuration, we construct analytical solutions to describe the system's temporal dynamics in the both interaction regimes. Further, we investigate the influence of inter-particle elastic scattering on the dynamics of coherent molecule formation subject to an external field configuration of the resonance-crossing Landau-Zener model. We derive an approximate solution which for the first time describes the whole temporal dynamics of the molecule formation in this general case.

Japanese encephalitis virus (JEV) causes viral encephalitis in new born and young adults that is prevalent in different parts of India and other parts of South East Asia with an estimated 6000 deaths per year. JEV is a single stranded RNA virus that belongs to the Flavivirusgenus of the family Flaviviridae. It is a neurotropic virus which infects the central nervous system (CNS). The virus follows a zoonotic life-cycle involving mosquitoes and vertebrates, chiefly pigs and ardeid birds, as amplifying hosts. Humans are dead end hosts. After entry into the host following a mosquito bite, JEV infection leads to acute peripheral leukocytosis in the brain and damage to Blood Brain Barrier (BBB). The exact role of the endothelial cells during CNS infection is still unclear. However, disruption of this endothelial barrier has been shown to be an important step in entry of the virus into the brain. Humoral and cell mediated immune responses during JEV infection have been intensively investigated. Previous studies from our lab have shown the activation of cytotoxic T-cells (CTLs) upon JEV infection. MHC molecules play pivotal role in eliciting both adaptive (T-cells) and innate (NK cells) immune response against viral invasion. Many viruses such as HIV, MCMV, HCMV, AdV and EBV have been found to decrease MHC expression upon infection. On the contrary, flaviviruses like West Nile Virus (WNV) have been found to increase MHC-I and MHC-II expression. More recently, data from our lab has shown that JEV infection can lead to upregulation of mouse non-classical MHC class Ib molecules like Qb1, Qa1 and T-10 along with classical MHC molecules. Non-classical MHC molecules are important components of the innate and adaptive immune systems. Non-classical MHC molecules differ from their classical MHC class I counterparts by their limited polymorphism, restricted tissue distribution and lower levels of cell surface expression. Human classical MHC class I molecules are HLA-A, -B and –C while non-classical MHC Class Ib molecules are HLA-E, -G and –F. HLA-E, the human homologue of the mouse non-classical MHC molecule, Qa-1b has been shown to be the ligand for the inhibitory NK, NKG2A/CD94 and may bridge innate and adaptive immune responses. In this thesis, we have studied the expression of human classical class I molecules HLA-A, -B, -C and the non-classical HLA molecule, HLA-E in immortalized human brain microvascular endothelial cells (HBMEC), human endothelial like cell line ECV304 (ECV), human glioblastoma cell line U87MG and human foreskin fibroblast cells (HFF). We observed an upregulation of classical HLA molecules and HLA-E mRNA in endothelial and fibroblast cells upon JEV infection. This mRNA increase also resulted in upregulation of cell surface classical HLA molecules and HLA-E in HFF cells but not in both the human endothelial cell lines, ECV and HBMECs. Release of soluble classical HLA molecules upon cytokine treatment has been a long known phenomenon. Recently HLA-E has also been shown to be released as a 37 kDa protein from endothelial cells upon cytokine treatments. Our study suggests that JEV mediated upregulation of classical HLA and HLA-E upregulation leads to release of both Classical HLA molecules and HLA-E as soluble forms in the human endothelial cell lines, ECV and HBMEC. This shedding of sHLA-E from human endothelial cells was found to be mediated by matrix metalloproteinase (MMP) proteolytic activity. MMP-9, a protease implicated in release of sHLA molecules was also found to be upregulated upon JEV infection only in endothelial cell lines but not in HFF cells. Our study provides evidence that the JEV mediated solubilisation of HLA-E could be mediated by MMP-9. Further, we have tried to understand the role of the MAPK pathway and NF-κB pathway in the process of HLA-E solubilisation by using specific inhibitors of these pathways during JEV infection of ECV cells. Our data suggests that release of sHLA-E is dependent on p38 and JNK pathways while ERK 1/2 and NF-κB pathway only had a minor role to play in this process. Treatment of endothelial cells with TNF-α, IL-1β and IFN-γ is known to result in release of sHLA-E. In addition to TNF-α and IFNtreatment, we observed that activating agents like poly (I:C), LPS and PMA also resulted in the shedding of sHLA-E from ECV as well as U87MG but not from HFF cells. Treatment of endothelial cells with IFN-β, a type-I interferon also led to release of sHLA-E. IFN-γ, a type II interferon and TNF-α are known to show additive increase in solubilisation of HLA-E. We studied the interaction between type I interferon, IFN-β and TNF-α with regard to shedding of sHLA- E. Both IFNand TNF, when present together caused an additive increase in the shedding of sHLA-E. These two cytokines were also found to potentiate the HLA-E and MMP-9 mRNA expression. Hence, our data suggest that these two cytokines could be working conjunctly to release HLA-E, when these two cytokines are present together as in the case of virus infection of endothelial cells. HLA-E is known to be a ligand for NKG2A/CD94 inhibitory receptors present on NK and a subset of T cells. Previous reports have suggested that NKG2A/CD94 mediated signaling events could inhibit ERK 1/2 phosphorylation leading to inhibition of NK cell activation. IL-2 mediated ERK 1/2 phosphorylation is known to play a very important role in maintenance and activation of NK cells. We studied the effects of sHLA-E that was released, either by JEV infection or IFN-γ treatment on IL-2 mediated ERK 1/2 phosphorylation in two NK cell lines, Nishi and NKL. The soluble HLA-E that was released upon JEV infection was functionally active since it inhibited IL-2 and PMA induced phosphorylation of ERK 1/2 in NKL and Nishi cells. Virus infected or IFN-γ treated ECV cell culture supernatants containing sHLA-E was also found to partially inhibit IL-2 mediated induction of CD25 molecules on NKL cells. CD25 is a component of the high affinity IL-2 receptor and hence could play an important role in proliferation and activation of NK cells. sHLA-E was also found to inhibit IL-2 induced [3H]-thymidine incorporation suggesting that, similar to cell surface expressed HLA-E, sHLA-E could also inhibit the proliferation and activation of NK cells. In summary, we found that establishment of JEV infection and production of cytokines like IFN-β, TNF-α, IL-6 along with MMP-9 in human endothelial cells. These cytokines may also indirectly lead to the reported damage and leukocyte infiltration across infected and uninfected vicinal endothelial cells. The increased surface expression of HLA-E in fibroblast and release of sHLA and sHLA-E molecules from endothelial cells may have an important immunoregulatory role. HLA-E is an inhibitory ligand for NKG2A/CD94 positive CD8+ T and NK cells. Hence our finding that sHLA-E can inhibit NK cell proliferation suggests an immune evasive strategy by JEV.

In this thesis, I have investigated gas phase infrared spectroscopy of environmentally as well as astrophysical important large organic molecules such as naphthalene, methy-lated naphthalene, fluorine, methyalted fluorine etc. which are commonly known as polycyclic aromatic hydrocarbons (PAHs). Depending upon the molecular weight these organic molecules can exist both in gaseous as well as in the particulate state at room temperature hence they are the major environmental pollutants. They are also responsible for the unidentified infrared emission bands in the interstellar medium. Chapter 1 provides a brief introduction to my thesis work. A detailed literature survey on the importance, abundance of the PAHs in the environment as well as various spectroscopic techniques useful for identifying the PAHs has been done. Since the objective of my thesis work is to assign the observed fundamental infrared bands of large organic molecules with the help of high level quantum mechanical calculations, a brief introduction to the various high level quantum mechanical techniques that I have used in assigning the bands have been described in this chapter. In Chapter 2 I have presented the experimental and the theoretical methodologies in details. The chapter begins with a detailed description of the experimental procedure used for recording the infrared spectrum of these molecules followed by the theoretical methodologies used for the assignment of the observed infrared bands as well as for identifying the Fermi resonances. In Chapters 3 and 4, of this thesis I have recorded infrared spectrum of 1-and 2-methylnaphthalene (1-and 2-MN), fluorine (FL), 1-methylfluorene (1-MFL) and 1,8-dimethylfluorene (1,8-DMF) in the gas phase. The observed bands were assigned with the help of scaled harmonic frequency, scaled quantum mechanical harmonic force field (SQMFF) and enharmonic frequency calculations. The first two methods are based on the harmonic approximation, whereas the enharmonic frequency calculation is based on the standard second order perturbation theory. All these calculations gave me a partial fit to the fundamental bands in both aromatic and aliphatic C-H stretching as well as in the non C-H stretching region. At the end of both the chapters an error analysis in fitting the spectrum from all the three different calculations have been presented. Evidently the non linear least square fitting method employed in SQMFF calculation gives much better agreement between the experiment and theory than the other two methods. It has been observed in the experimental spectrum of methylated naphthalene that the band structure near the C-H stretch around 3000 cm−1 is very complicated and many bands and shoulders remain unassigned by the methods described in Chapters 3 and 4. Fermi resonance is one of the potential reason for the complicated band structure in this region. In Chapter 5, I have taken naphthalene and have investigated the Fermi resonance around the C-H stretching region using an effective vibrational hamiltonian (EVH) approach. In this method I have constructed an EVH consisting of 8 C-H stretches and 8 H-C-C in-plane bend overtones and 28 H-C-C in-plane bend combination modes as the basis. Both type 1 (stretch overtone) and type 2 (stretch combination) Fermi resonances were investigated. Calculated frequencies belonging to B1u and B2u irreducible representation were compared with the observed bands. Many bands and shoulders have been assigned as the overtone and combination modes of low frequency H-C-C bend motion obtained from the EVH approach. How-ever some bands remain unassigned in this method. This is perhaps due to the neglect of the carbon framework motion in the construction of the EVH. To improve upon the results obtained from the EVH formalism I included the carbon frame degrees of freedom and have carried out a full variation treatment in curvilinear coordinates. I have considered the 8 C-H stretches and 8 H-C-C in-plane bends of naphthalene as local mode oscillators and 17 coordinates belonging to the carbon framework motion as curvilinear normal mode oscillators. A quartic hamiltonian in a mixed local mode -normal mode basis was constructed including up to three body terms in both kinetic and potential energy part. The hamiltonian was subsequently recast into the ladder operator form and diagonal zed in a symmetry adapted basis with polyad constraints. Frequencies so obtained were compared to the experiment All these findings have been presented in Chapter 6 of this thesis. The concluding remark of the thesis and the future direction is presented in Chapter 7

L'étude de l'ionisation de molécules biologiques, bases de l'ADN et de l'ARN, par impact de protons (20-150 keV/uma) a été l'enjeu de ce travail. Les expériences développées ont permis d'étudier la fragmentation de l'uracile, la thymine, l'adénine et la cytosine sous impact de protons, et de développer une méthode de mesure de section efficace absolue des processus d'ionisation mis en jeu au cours de l'interaction proton-molécule cible.<br />Le dispositif expérimental développé a permis de séparer les contributions des deux processus d'ionisation de la molécule cible : l'ionisation directe et l'ionisation par capture électronique. Les spectres de masse correspondants, analysés événement par événement, ont été mesurés. Pour l'uracile, les rapports de branchement de ces deux processus ont été mesurés en fonction de la vitesse du projectile.<br />Nous avons développé la mesure de sections efficaces absolues pour le processus de capture électronique. Le taux de production d'atomes neutres par rapport au nombre de protons incidents a été mesuré pour les quatre molécules étudiées : uracile, cytosine, thymine et adénine, et ceci, pour différentes températures d'évaporation. Ce taux varie avec l'épaisseur de cible traversée par le faisceau de protons. Un dispositif de dépôt a été développé pour caractériser la densité moléculaire du jet gazeux des bases étudiées. L'étude théorique et expérimentale du débit total d'effusion et du profil du jet gazeux a permis de déduire l'épaisseur de cible traversée par le faisceau de protons. Ainsi, la section efficace absolue d'ionisation des quatre molécules biologiques isolées sous impact de protons d'énergie de 80 keV/uma a été déterminée.