Phosphatidylserine-containing liposomes:modulators of rhinovirus induced inflammatory responses

Background: Human rhinoviral infections are major contributors to the healthcare burden associated with acute exacerbations of asthma. We, and others have recently demonstrated that rhinovirus (RV)-induced inflammatory responses are mediated by multiple signalling mechanisms, such as IL-1/MyD88 (1) and TLR3/RIGI (2). We have also previously published work showing that TLR signalling is effectively inhibited by phosphatidylserine-containing liposomes (SAPS), through the disruption of membrane microdomains (3). Evidence has also suggested that membrane microdomains may influence infections with RV. In this study, we explored the ability of SAPS to modulate responses to the natural viral pathogens, RV-1B and RV-16. Method: The immortalized bronchial epithelial cell line, BEAS-2B or primary bronchial epithelial cells were infected with RV-1B or RV-16 at a TCID50/ml of 19107 for 1 h. Immediately following infection, various concentrations of SAPS were added and changes in cytokine release were measured at 24 h. SAPS remained present throughout. Type I and III interferon (IFN) expression and rates of viral replication were measured by quantitative PCR. Virus quantification was also performed using a viral CPE assay, and IFN signalling was measured by western blot. Liposome stability was characterised and intracellular trafficking of fluorescently labelled SAPS in BEAS-2B cells was investigated using confocal microscopy. For in vivo studies, female wt Balb/c mice were pre-treated with SAPS for 2 h prior to infection with RV as previously described and changes in BAL cell number, BAL cytokine production and viral replication were quantified (4). Results: Characterisation of SAPS liposomes by mass spectrometry showed no obvious signs of oxidation over the time period tested, and liposome size remained constant. Preliminary confocal studies revealed that SAPS was rapidly internalised within the cell and was found to associate with intracellular compartments such as the early endosome and golgi. Viral infected BEAS-2B cells co-incubated with SAPS, showed notably impaired responses to RV as assessed by release of CXCL8 and CCL5. SAPS also reduced RV-induced IFNb production and STAT-1 phosphorylation, without significantly influencing viral replication rates. Modest increases in viral particle production were only observed at 48 and 72 h time points. Suppression of viral-induced cytokine production was also observed in primary bronchial epithelial cells and pilot in vivo studies showed that SAPS results in reduced KC production at 24 h post viral infection, and this was associated with reduced neutrophil numbers within the BAL fluid. Conclusion: Our data demonstrates a potential means of modulating inflammatory responses induced by human rhinovirus.

Spectral characteristics and thermal evolution of long-period gratings in photonic crystal fibers fabricated with a near-IR radiation femtosecond laser using point-by-point inscription

The spectral properties of long-period gratings (LPGs) fabricated in photonic crystal fibers using femtosecond laser pulses by the point-by-point technique, without oil-immersion of the fiber, are investigated in detail. Postfabrication spectral monitoring at room temperature showed significant long-term instability of the gratings and stable spectra only after 600 h. The stabilized spectral properties of the gratings improved with increasing annealing temperature. The observed changes in resonant wavelength, optical strength, and grating birefringence were correlated to the laser inscription energy and were further used to study the mechanism of femtosecond inscription. Furthermore, the femtosecond-laser inscribed LPGs were compared to electric-arc fabricated LPGs. Comparison of experimental results with theoretical models of LPGs and laser propagation during inscription indicate that the major processes responsible for the index change are permanent compaction and thermally induced strain, the latter can be significantly changed through annealing. © 2011 Optical Society of America.

Characterization of polymer fiber Bragg grating with ultrafast laser micromachining

We report that the main photosensitive mechanism of poly(methyl methacrylate)-based optical fiber Bragg grating (POFBG) under ultraviolet laser micromachining is a complex process of both photodegradation and negative thermo-optic effect. We found experimentally the unique characteristics of Bragg resonance splitting and reunion during the laser micromachining process providing the evidence of photodegradation, while the mean refractive index change of POFBG was measured to be negative confirming further photodegradation of polymer fiber. The thermal-induced refractive index change of POFBG was also observed by recording the Bragg wavelength shift. Furthermore, the dynamic thermal response of the micromachined-POFBG was demonstrated under constant humidity, showing a linear and negative response of around -47.1 pm/°C.

The redoxomics of PTEN: walking a fine line between damage and signaling:mass spectrometry-based approaches to study the effect of oxidation on PTEN function, structure, and protein-protein interactions

The research described in this PhD thesis focuses on proteomics approaches to study the effect of oxidation on the modification status and protein-protein interactions of PTEN, a redox-sensitive phosphatase involved in a number of cellular processes including metabolism, apoptosis, cell proliferation, and survival. While direct evidence of a redox regulation of PTEN and its downstream signaling has been reported, the effect of cellular oxidative stress or direct PTEN oxidation on PTEN structure and interactome is still poorly defined. In a first study, GST-tagged PTEN was directly oxidized over a range of hypochlorous acid (HOCl) concentration, assayed for phosphatase activity, and oxidative post-translational modifications (oxPTMs) were quantified using LC-MS/MS-based label-free methods. In a second study, GSTtagged PTEN was prepared in a reduced and reversibly H2O2-oxidized form, immobilized on a resin support and incubated with HCT116 cell lysate to capture PTEN interacting proteins, which were analyzed by LC-MS/MS and comparatively quantified using label-free methods. In parallel experiments, HCT116 cells transfected with a GFP-tagged PTEN were treated with H2O2 and PTENinteracting proteins immunoprecipitated using standard methods. Several high abundance HOCl-induced oxPTMs were mapped, including those taking place at amino acids known to be important for PTEN phosphatase activity and protein-protein interactions, such as Met35, Tyr155, Tyr240 and Tyr315. A PTEN redox interactome was also characterized, which identified a number of PTEN-interacting proteins that vary with the reversible inactivation of PTEN caused by H2O2 oxidation. These included new PTEN interactors as well as the redox proteins peroxiredoxin-1 (Prdx1) and thioredoxin (Trx), which are known to be involved in the recycling of PTEN active site following H2O2-induced reversible inactivation. The results suggest that the oxidative modification of PTEN causes functional alterations in PTEN structure and interactome, with fundamental implications for the PTEN signaling role in many cellular processes, such as those involved in the pathophysiology of disease and ageing.

Raman fibre laser based amplification in coherent transmission systems

The thesis presents a detailed study of different Raman fibre laser (RFL) based amplification techniques and their applications in long-haul/unrepeatered coherent transmission systems. RFL based amplifications techniques were characterised from different aspects, including signal/noise power distributions, relative intensity noise (RIN), mode structures of induced Raman fibre lasers, and so on. It was found for the first time that RFL based amplification techniques could be divided into three categories in terms of the fibre laser regime, which were Fabry-Perot fibre laser with two FBGs, weak Fabry-Perot fibre laser with one FBG and very low reflection near the input, and random distributed feedback (DFB) fibre laser with one FBG. It was also found that lowering the reflection near the input could mitigate the RIN of the signal significantly, thanks to the reduced efficiency of the Stokes shift from the FW-propagated pump. In order to evaluate the transmission performance, different RFL based amplifiers were evaluated and optimised in long-haul coherent transmission systems. The results showed that Fabry-Perot fibre laser based amplifier with two FBGs gave >4.15 dB Q factor penalty using symmetrical bidirectional pumping, as the RIN of the signal was increased significantly. However, random distributed feedback fibre laser based amplifier with one FBG could mitigate the RIN of the signal, which enabled the use of bidirectional second order pumping and consequently give the best transmission performance up to 7915 km. Furthermore, using random DFB fibre laser based amplifier was proved to be effective to combat the nonlinear impairment, and the maximum reach was enhanced by >28% in mid-link single/dual band optical phase conjugator (OPC) transmission systems. In addition, unrepeatered transmission over >350 km fibre length using RFL based amplification technique were presented experimentally using DP-QPSK and DP-16QAM transmitter.

Nonlinear optical effects manifested by electromagnetic induced transparency in cold atoms

This dissertation reports experimental studies of nonlinear optical effects manifested by electromagnetically induced transparency (EIT) in cold Rb atoms. The cold Rb atoms are confined in a magneto-optic trap (MOT) obtained with the standard laser cooling and trapping technique. Because of the near zero Doppler shift and a high phase density, the cold Rb sample is well suited for studies of atomic coherence and interference and related applications, and the experiments can be compared quantitatively with theoretical calculations. It is shown that with EIT induced in the multi-level Rb system by laser fields, the linear absorption is suppressed and the nonlinear susceptibility is enhanced, which enables studies of nonlinear optics in the cold atoms with slow photons and at low light intensities. Three independent experiments are described and the experimental results are presented. First, an experimental method that can produce simultaneously co-propagating slow and fast light pulses is discussed and the experimental demonstration is reported. Second, it is shown that in a three-level Rb system coupled by multi-color laser fields, the multi-channel two-photon Raman transitions can be manipulated by the relative phase and frequency of a control laser field. Third, a scheme for all-optical switching near single photon levels is developed. The scheme is based on the phase-dependent multi-photon interference in a coherently coupled four-level system. The phase dependent multi-photon interference is observed and switching of a single light pulse by a control pulse containing ∼20 photons is demonstrated. These experimental studies reveal new phenomena manifested by quantum coherence and interference in cold atoms, contribute to the advancement of fundamental quantum optics and nonlinear optics at ultra-low light intensities, and may lead to the development of new techniques to control quantum states of atoms and photons, which will be useful for applications in quantum measurements and quantum photonic devices.

Functional genomic and molecular analyses of transcripts related to glycerol synthesis and trafficking in rainbow smelt (Osmerus mordax) using cold temperature-induced models of glycerol production

The rainbow smelt (Osmerus mordax) is an anadromous teleost that produces type II antifreeze protein (AFP) and accumulates modest urea and high glycerol levels in plasma and tissues as adaptive cryoprotectant mechanisms in sub-zero temperatures. It is known that glyceroneogenesis occurs in liver via a branch in glycolysis and gluconeogenesis and is activated by low temperature; however, the precise mechanisms of glycerol synthesis and trafficking in smelt remain to be elucidated. The objective of this thesis was to provide further insight using functional genomic techniques [e.g. suppression subtractive hybridization (SSH) cDNA library construction, microarray analyses] and molecular analyses [e.g. cloning, quantitative reverse transcription - polymerase chain reaction (QPCR)]. Novel molecular mechanisms related to glyceroneogenesis were deciphered by comparing the transcript expression profiles of glycerol (cold temperature) and non-glycerol (warm temperature) accumulating hepatocytes (Chapter 2) and livers from intact smelt (Chapter 3). Briefly, glycerol synthesis can be initiated from both amino acids and carbohydrate; however carbohydrate appears to be the preferred source when it is readily available. In glycerol accumulating hepatocytes, levels of the hepatic glucose transporter (GLUT2) plummeted and transcript levels of a suite of genes (PEPCK, MDH2, AAT2, GDH and AQP9) associated with the mobilization of amino acids to fuel glycerol synthesis were all transiently higher. In contrast, in glycerol accumulating livers from intact smelt, glycerol synthesis was primarily fuelled by glycogen degradation with higher PGM and PFK (glycolysis) transcript levels. Whether initiated from amino acids or carbohydrate, there were common metabolic underpinnings. Increased PDK2 (an inhibitor of PDH) transcript levels would direct pyruvate derived from amino acids and / or DHAP derived from G6P to glycerol as opposed to oxidation via the citric acid cycle. Robust LIPL (triglyceride catabolism) transcript levels would provide free fatty acids that could be oxidized to fuel ATP synthesis. Increased cGPDH (glyceroneogenesis) transcript levels were not required for increased glycerol production, suggesting that regulation is more likely by post-translational modification. Finally, levels of a transcript potentially encoding glycerol-3-phosphatase, an enzyme not yet characterized in any vertebrate species, were transiently higher. These comparisons also led to the novel discoveries that increased G6Pase (glucose synthesis) and increased GS (glutamine synthesis) transcript levels were part of the low temperature response in smelt. Glucose may provide increased colligative protection against freezing; whereas glutamine could serve to store nitrogen released from amino acid catabolism in a non-toxic form and / or be used to synthesize urea via purine synthesis-uricolysis. Novel key aspects of cryoprotectant osmolyte (glycerol and urea) trafficking were elucidated by cloning and characterizing three aquaglyceroporin (GLP)-encoding genes from smelt at the gene and cDNA levels in Chapter 4. GLPs are integral membrane proteins that facilitate passive movement of water, glycerol and urea across cellular membranes. The highlight was the discovery that AQP10ba transcript levels always increase in posterior kidney only at low temperature. This AQP10b gene paralogue may have evolved to aid in the reabsorption of urea from the proximal tubule. This research has contributed significantly to a general understanding of the cold adaptation response in smelt, and more specifically to the development of a working scenario for the mechanisms involved in glycerol synthesis and trafficking in this species.

Dynamics of vector rogue waves in a fiber laser with a ring cavity

A pulse–pulse interaction that leads to rogue wave (RW) generation in lasers was previously attributed either to soliton–soliton or soliton–dispersive-wave interaction. The beating between polarization modes in the absence of a saturable absorber causes similar effects. Accounting for these polarization modes in a laser resonator is the purpose of the distributed vector model of laser resonators. Furthermore, high pump power, high amplitude, and short pulse duration are not necessary conditions to observe pulse attraction, repulsion, and collisions and the resonance exchange of energy between among them. The regimes of interest can be tuned just by changing the birefringence in the cavity with the pump power slightly higher than the laser threshold. This allows the observation of a wide range of RW patterns in the same experiment, as well as to classify them. The dynamics of the interaction between pulses leads us to the conclusion that all of these effects occur due to nonlinearity induced by the inverse population in the active fiber as well as an intrinsic nonlinearity in the passive part of the cavity. Most of the mechanisms of pulse–pulse interaction were found to be mutually exclusive. This means that all the observed RW patterns, namely, the “lonely,” “twins,” “three sisters,” and “cross,” are probably different cases of the same process.

Temporal scaling of optical rogue waves in unidirectional ring fiber laser

A fiber mode-lock laser allows generation of the optical rogue wave (ORW) at different time scales. The criteria for distinguishing between them is a comparison of the event lifetime with the main characteristic time of the system. The characteristic time can be estimated from the decay of an autocorrelation function (AF). Thus, in comparison with AF characteristic time, fast optical rogue wave (FORW) events have duration less than the AF decay time and it appeared due to pulse-pulse interaction and nonlinear pulses dynamics. While slow optical rogue wave (SORW) have a duration much more longer than the decay time of the AF which it papered due to hopping between different attractors. Switching between regimes can be managed by change the artificial birefringence that induced in a laser cavity. For understanding the role playing by the periodical amplification and the resonator, we have performed an unidirectional fiber laser experiments without a saturable absorber. This laser experiment allowed to generate of most of the RW patterns which were either observed experimentally or predicted theoretically. In this way, we have observed the generation of an FORW along with SORW under similar conditions. Most of the patterns were found to be mutually exclusive which means that only one RW mechanism was realized in each regime of generation.

Flat-top supercontinuum and tunable femtosecond fiber laser sources at 1.9-2.5 μm

We report the high-energy flat-top supercontinuum covering the mid-infrared wavelength range of 1.9-2.5 μm as well as electronically tunable femtosecond pulses between 1.98-2.22 μm directly from the thulium-doped fiber laser amplifier. Comparison of experimental results with numerical simulations confirms that both sources employ the same nonlinear optical mechanism - Raman soliton frequency shift occurring inside the Tm-fiber amplifier. To illustrate that, we investigate two versions of the compact diode-pumped SESAM mode-locked femtosecond thulium-doped all-silica-fiber-based laser system providing either broadband supercontinuum or tunable Raman soliton output, depending on the parameters of the system. The first system operates in the Raman soliton regime providing femtosecond pulses tunable between 1.98-2.22 μm. Wide and continuous spectral tunability over 240 nm was realized by changing only the amplifier pump diode current. The second system generates high-energy supercontinuum with the superior spectral flatness of better than 1 dB covering the wavelength range of 1.9-2.5 μm, with the total output energy as high as 0.284 μJ, the average power of 2.1 W at 7.5 MHz repetition rate. We simulate the amplifier operation in the Raman soliton self-frequency shift regime and discuss the role of induced Raman scattering in supercontinuum formation inside the fiber amplifier. We compare this system with a more traditional 1.85-2.53 μm supercontinuum source in the external highly-nonlinear commercial chalcogenide fiber using the Raman soliton MOPA as an excitation source. The reported systems1 can be readily applied to a number of industrial applications in the mid-IR, including sensing, stand-off detection, medical surgery and fine material processing.

Charge migration induced by attosecond pulses in bio-relevant molecules

After sudden ionization of a large molecule, the positive charge can migrate throughout the system on a sub-femtosecond time scale, purely guided by electronic coherences. The possibility to actively explore the role of the electron dynamics in the photo-chemistry of bio-relevant molecules is of fundamental interest for understanding, and perhaps ultimately controlling, the processes leading to damage, mutation and, more generally, to the alteration of the biological functions of the macromolecule. Attosecond laser sources can provide the extreme time resolution required to follow this ultrafast charge flow. In this review we will present recent advances in attosecond molecular science: after a brief description of the results obtained for small molecules, recent experimental and theoretical findings on charge migration in bio-relevant molecules will be discussed.

Towards optical polarization control of laser-driven proton acceleration in foils undergoing relativistic transparency

Control of the collective response of plasma particles to intense laser light is intrinsic to relativistic optics, the development of compact laser-driven particle and radiation sources, as well as investigations of some laboratory astrophysics phenomena. We recently demonstrated that a relativistic plasma aperture produced in an ultra-thin foil at the focus of intense laser radiation can induce diffraction, enabling polarization-based control of the collective motion of plasma electrons. Here we show that under these conditions the electron dynamics are mapped into the beam of protons accelerated via strong charge-separation-induced electrostatic fields. It is demonstrated experimentally and numerically via 3D particle-in-cell simulations that the degree of ellipticity of the laser polarization strongly influences the spatial-intensity distribution of the beam of multi-MeV protons. The influence on both sheath-accelerated and radiation pressure-accelerated protons is investigated. This approach opens up a potential new route to control laser-driven ion sources.

Photochemical dynamics of laser-irradiated semiconductor nanostructures

Thesis (Ph.D.)--University of Washington, 2016-08

DNA damage induced by low energy electrons (LEEs)

Abstract : The major objective of our study is to investigate DNA damage induced by soft X-rays (1.5 keV) and low-energy electrons (˂ 30 eV) using a novel irradiation system created by Prof. Sanche’s group. Thin films of double-stranded DNA are deposited on either glass and tantalum substrates and irradiated under standard temperature and pressure surrounded by a N[subscript 2] environment. Base release (cytosine, thymine, adenine and guanine) and base modifications (8-oxo-7,8-dihydro -2’-deoxyguanosine, 5-hydroxymethyl-2’-deoxyuridine, 5-formyl-2’-deoxyuridine, 5,6-dihydrothymidine and 5,6-dihydro-2’-deoxy uridine) are analyzed and quantified by LC-MS/MS. Our results reveal larger damage yields in the sample deposited on tantalum than those on glass. This can be explained by an enhancement of damage due to low-energy electrons, which are emitted from the metal substrate. From a comparison of the yield of products, base release is the major type of damage especially for purine bases, which are 3-fold greater than base modifications. A proposed pathway leading to base release involves the formation of a transient negative ion (TNI) followed by dissociative electron attachment (DEA) at the N-g lycosidic bond. On the other hand, base modification products consist of two major types of chemical modifications, which include thymine methyl oxidation products that likely arises from DEA from the methyl group of thymine, and 5,6-dihydropyrimidine that can involve the initial addition of electrons, H atoms, or hydride ions to the 5,6-pyrimidine double bond.

Ordering induced by chemical, thermal and mechanical constraints at solid interfaces

We know that classical thermodynamics even out of equilibrium always leads to stable situation which means degradation and consequently d sorder. Many experimental evidences in different fields show that gradation and order (symmetry breaking) during time and space evolution may appear when maintaining the system far from equilibrium. Order through fluctuations, stochastic processes which occur around critical points and dissipative structures are the fundamental background of the Prigogine-Glansdorff and Nicolis theory. The thermodynamics of macroscopic fluctuations to stochastic approach as well as the kinetic deterministic laws allow a better understanding of the peculiar fascinating behavior of organized matter. The reason for the occurence of this situation is directly related to intrinsic non linearities of the different mechanisms responsible for the evolution of the system. Moreover, when dealing with interfaces separating two immiscible phases (liquid - gas, liquid -liquid, liquid - solid, solid - solid), the situation is rather more complicated. Indeed coupling terms playing the major role in the conditions of instability arise from the peculiar singular static and dynamic properties of the surface and of its vicinity. In other words, the non linearities are not only intrinsic to classical steps involving feedbacks, but they may be imbedded with the non-autonomous character of the surface properties. In order to illustrate our goal we discuss three examples of ordering in far from equilibrium conditions: i) formation of chemical structures during the oxidation of metals and alloys; ii) formation of mechanical structures during the oxidation of metals iii) formation of patterns at a solid-liquid moving interface due to supercooling condition in a melt of alloy. © 1984, Walter de Gruyter. All rights reserved.