Characterization of cation exchanger stationary phases applied for the separations of therapeutic monoclonal antibodies.

Cation exchange chromatography (CEX) is a well established strategy for the characterization of monoclonal antibodies (mAbs). The optimization of mobile phase conditions is well described in the literature, but there is a lack of information about CEX stationary phases for the analysis of therapeutic proteins. The aim of this study was to compare five state-of-the-art CEX stationary phases based on the retention, selectivity and resolving power achieved in pH- and salt-gradient modes, with various therapeutic mAbs and their variants. The Sepax Antibodix WCX-NP3, Thermo MAbPac SCX-10 RS, YMC BioPro SP-F, Waters Protein-Pak Hi Res SP and Agilent Bio mAb NP1.7 SS were considered in this study. In terms of retention, the YMC Bio Pro SP-F material was the less retentive one, while the Agilent Bio mAb NP1.7 SS provides the highest retention. Regarding the selectivity achieved between the main mAbs isoforms and their variants, the Thermo MabPac SCX column generally gave the highest selectivity. Finally, it was hard to rank columns in term of kinetic performance since their performance is strongly solute (mAb) and elution mode (pH or salt gradient) dependent. However, the highest resolution--in most cases--was observed on the strong cation exchanger YMC Bio Pro SP-F material.

Euphorbia tirucalli L.–Comprehensive Characterization of a Drought Tolerant Plant with a Potential as Biofuel Source

Of late, decrease in mineral oil supplies has stimulated research on use of biomass as an alternative energy source. Climate change has brought problems such as increased drought and erratic rains. This, together with a rise in land degeneration problems with concomitant loss in soil fertility has inspired the scientific world to look for alternative bio-energy species. Euphorbia tirucalli L., a tree with C3/CAM metabolism in leaves/stem, can be cultivated on marginal, arid land and could be a good alternative source of biofuel. We analyzed a broad variety of E. tirucalli plants collected from different countries for their genetic diversity using AFLP. Physiological responses to induced drought stress were determined in a number of genotypes by monitoring growth parameters and influence on photosynthesis. For future breeding of economically interesting genotypes, rubber content and biogas production were quantified. Cluster analysis shows that the studied genotypes are divided into two groups, African and mostly non-African genotypes. Different genotypes respond significantly different to various levels of water. Malate measurement indicates that there is induction of CAM in leaves following drought stress. Rubber content varies strongly between genotypes. An investigation of the biogas production capacities of six E. tirucalli genotypes reveals biogas yields higher than from rapeseed but lower than maize silage.

Synthesis and Characterization of Nanostructured Electro-active Materials

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

Protemic characterization of peripheral blood mononuclear cells

Peripheral blood mononuclear cells (PBMCs) play quite diverse and important roles in monitoring immune homeostasis. Thus, these subset of blood cells may provide access to potential physiological relevant biomolecules, namely proteins. For this reason, PBMCs represent a promising biological sample in scientific research, particularly as a source of potential biological markers discovery of the most diverse diseases. Prior studies of proteomic characterization of PBMCs from healthy individuals lack either the identification of a large number of proteins or its quantification in a way that is compatible with the search of potential biomarker candidates. Therefore, this study aimed to provide a comprehensive PBMCs proteome characterisation as well as to create a SWATH library. It was also evaluated if by using the BD Vacutainer® CPT™ tubes for PBMCs isolation, it would be possible to identify a larger number of immunologically relevant proteins in comparison to plasma samples. The enrichment test assay revealed that it is possible to identify more immune-related proteins from isolated PBMCs than from plasma. Moreover, the majority of the quantified proteins with an “immune system” GO term assigned is present in higher amounts in PBMCs samples. 2D LC-MS/MS proved to be the best approach to use in qualitative analysis of PBMCs and in the construction of a SWATH library, since it resulted in an increase of both identified and quantified proteins (66.3% and 16.9%, respectively) in comparison to 1D LC-MS/MS. A total of 2071 proteins were identified and it was possible to quantify 922 different proteins among six distinct samples. From these proteins, 445 were commom between all individuals. In conclusion, this work provides a comprehensive PBMCs proteome dataset that will be useful in further studies that focus on the search for potential biological markers of various pathologies in these cells. Additionally, SWATH-MS proved to be a reproducible and effective acquisition method to quantify PBMCs proteins.

DESIGN, FABRICATION, AND PERFORMANCE CHARACTERIZATION OF MULTIFUNCTIONAL STRUCTURES TO HARVEST SOLAR ENERGY FOR FLAPPING WING AERIAL VEHICLES

Flapping Wing Aerial Vehicles (FWAVs) have the capability to combine the benefits of both fixed wing vehicles and rotary vehicles. However, flight time is limited due to limited on-board energy storage capacity. For most Unmanned Aerial Vehicle (UAV) operators, frequent recharging of the batteries is not ideal due to lack of nearby electrical outlets. This imposes serious limitations on FWAV flights. The approach taken to extend the flight time of UAVs was to integrate photovoltaic solar cells onto different structures of the vehicle to harvest and use energy from the sun. Integration of the solar cells can greatly improve the energy capacity of an UAV; however, this integration does effect the performance of the UAV and especially FWAVs. The integration of solar cells affects the ability of the vehicle to produce the aerodynamic forces necessary to maintain flight. This PhD dissertation characterizes the effects of solar cell integration on the performance of a FWAV. Robo Raven, a recently developed FWAV, is used as the platform for this work. An additive manufacturing technique was developed to integrate photovoltaic solar cells into the wing and tail structures of the vehicle. An approach to characterizing the effects of solar cell integration to the wings, tail, and body of the UAV is also described. This approach includes measurement of aerodynamic forces generated by the vehicle and measurements of the wing shape during the flapping cycle using Digital Image Correlation. Various changes to wing, body, and tail design are investigated and changes in performance for each design are measured. The electrical performance from the solar cells is also characterized. A new multifunctional performance model was formulated that describes how integration of solar cells influences the flight performance. Aerodynamic models were developed to describe effects of solar cell integration force production and performance of the FWAV. Thus, performance changes can be predicted depending on changes in design. Sensing capabilities of the solar cells were also discovered and correlated to the deformation of the wing. This demonstrated that the solar cells were capable of: (1) Lightweight and flexible structure to generate aerodynamic forces, (2) Energy harvesting to extend operational time and autonomy, (3) Sensing of an aerodynamic force associated with wing deformation. Finally, different flexible photovoltaic materials with higher efficiencies are investigated, which enable the multifunctional wings to provide enough solar power to keep the FWAV aloft without batteries as long as there is enough sunlight to power the vehicle.

FUNCTIONAL CHARACTERIZATION OF THE LINK BETWEEN CARBOHYDRATE METABOLISM AND THE PATHOGENESIS OF THE INVASIVE M1T1 GROUP A STREPTOCOCCUS

The Group A Streptococcus (GAS), or Streptococcus pyogenes, is a strict human pathogen that colonizes a variety of sites within the host. Infections can vary from minor and easily treatable, to life-threatening, invasive forms of disease. In order to adapt to niches, GAS utilizes environmental cues, such as carbohydrates, to coordinate the expression of virulence factors. Research efforts to date have focused on identifying how either components of the phosphoenolpyruvate-phosphotransferase system (PTS) or global transcriptional networks affect the regulation of virulence factors, but not the synergistic relationship between the two. The present study investigates the role of a putative PTS-fructose operon encoded by fruRBA and its role in virulence in the M1T1 strain 5448. Growth in fructose resulted in induction of fruRBA. RT-PCR showed that fruRBA formed an operon, which was repressed by FruR in the absence of fructose. Growth and carbon utilization profiles revealed that although the entire fruRBA operon was required for growth in fructose, FruA was the main fructose transporter. The ability of both ΔfruR and ΔfruB mutants to survive in whole human blood or neutrophils was impaired. However, the phenotypes were not reproduced in murine whole blood or in a mouse intraperitoneal infection, indicating a human-specific mechanism. While it is known that the PTS can affect activity of the Mga virulence regulator, further characterization of the mechanism by which sugars and its protein domains affect activity have not been studied. Transcriptional studies revealed that the core Mga regulon is activated more in a glucose-rich than a glucose-poor environment. This activation correlates with the differential phosphorylation of Mga at its PTS regulatory domains (PRDs). Using a 5448 mga mutant, transcriptome studies in THY or C media established that the Mga regulon reflects the media used. Interestingly, Mga regulates phage-encoded DNases in a low glucose environment. We also show that Mga activity is dependent on C-terminal amino acid interactions that aid in the formation of homodimers. Overall, the studies presented sought to define how external environmental cues, specifically carbohydrates, control complex regulatory networks used by GAS, contribute to pathogenesis, and aid in adaptation to various nutrient conditions encountered.

Characterization of Non-linear Polymer Properties to Predict Process Induced Warpage and Residual Stress of Electronic Packages

Nonlinear thermo-mechanical properties of advanced polymers are crucial to accurate prediction of the process induced warpage and residual stress of electronics packages. The Fiber Bragg grating (FBG) sensor based method is advanced and implemented to determine temperature and time dependent nonlinear properties. The FBG sensor is embedded in the center of the cylindrical specimen, which deforms together with the specimen. The strains of the specimen at different loading conditions are monitored by the FBG sensor. Two main sources of the warpage are considered: curing induced warpage and coefficient of thermal expansion (CTE) mismatch induced warpage. The effective chemical shrinkage and the equilibrium modulus are needed for the curing induced warpage prediction. Considering various polymeric materials used in microelectronic packages, unique curing setups and procedures are developed for elastomers (extremely low modulus, medium viscosity, room temperature curing), underfill materials (medium modulus, low viscosity, high temperature curing), and epoxy molding compound (EMC: high modulus, high viscosity, high temperature pressure curing), most notably, (1) zero-constraint mold for elastomers; (2) a two-stage curing procedure for underfill materials and (3) an air-cylinder based novel setup for EMC. For the CTE mismatch induced warpage, the temperature dependent CTE and the comprehensive viscoelastic properties are measured. The cured cylindrical specimen with a FBG sensor embedded in the center is further used for viscoelastic property measurements. A uni-axial compressive loading is applied to the specimen to measure the time dependent Young’s modulus. The test is repeated from room temperature to the reflow temperature to capture the time-temperature dependent Young’s modulus. A separate high pressure system is developed for the bulk modulus measurement. The time temperature dependent bulk modulus is measured at the same temperatures as the Young’s modulus. The master curve of the Young’s modulus and bulk modulus of the EMC is created and a single set of the shift factors is determined from the time temperature superposition. The supplementary experiments are conducted to verify the validity of the assumptions associated with the linear viscoelasticity. The measured time-temperature dependent properties are further verified by a shadow moiré and Twyman/Green test.

Low temperature magneto-photoluminescence characterization of high purity gallium arsenide and indium phosphide

Low-temperature magneto-photoluminescence is a very powerful technique to characterize high purity GaAs and InP grown by various epitaxial techniques. These III-V compound semiconductor materials are used in a wide variety of electronic, optoelectronic and microwave devices. The large binding energy differences of acceptors in GaAs and InP make possible the identification of those impurities by low-temperature photoluminescence without the use of any magnetic field. However, the sensitivity and resolution provided by this technique rema1ns inadequate to resolve the minute binding energy differences of donors in GaAs and InP. To achieve higher sensitivity and resolution needed for the identification of donors, a magneto-photoluminescence system 1s installed along with a tunable dye laser, which provides resonant excitation. Donors 1n high purity GaAs are identified from the magnetic splittings of "two-electron" satellites of donor bound exciton transitions 1n a high magnetic field and at liquid helium temperature. This technique 1s successfully used to identify donors 1n n-type GaAs as well as 1n p-type GaAs in which donors cannot be identified by any other technique. The technique is also employed to identify donors in high purity InP. The amphoteric incorporation of Si and Ge impurities as donors and acceptors in (100), (311)A and (3ll)B GaAs grown by molecular beam epitaxy is studied spectroscopically. The hydrogen passivation of C acceptors in high purity GaAs grown by molecular beam epitaxy (MBE) and metalorganic chemical vapor deposition (MOCVD) 1s investigated using photoluminescence. Si acceptors ~n MBE GaAs are also found to be passivated by hydrogenation. The instabilities in the passivation of acceptor impurities are observed for the exposure of those samples to light. Very high purity MOCVD InP samples with extremely high mobility are characterized by both electrical and optical techniques. It is determined that C is not typically incorporated as a residual acceptor ~n high purity MOCVD InP. Finally, GaAs on Si, single quantum well, and multiple quantum well heterostructures, which are fabricated from III-V semiconductors, are also measured by low-temperature photoluminescence.

Characterization of Borrelia burgdorferi Gene Product BBD18 for Its Role(s) in Pathogen Biology and Infectivity

bbd18 is a differentially expressed Borrelia burgdorferi gene that is transcribed at almost undetectable levels in spirochetes grown in vitro but dramatically upregulated during tick infection. The gene also displays low yet detectable expression at various times in tissues of murine hosts. As the gene product bears no homology to known proteins, its biological significance remains enigmatic. To understand the gene function, we created isogenic bbd18-deletion mutants as well as genetically-complemented isolates from an infectious wild-type B. burgdorferi strain. Compared to parental isolates, bbd18 mutants - but not complemented spirochetes - displayed slower in vitro growth. The bbd18 mutants also reflect significantly reduced ability to persist or remain undetectable both in immunocompetent and SCID mice, yet were able to survive in ticks. This suggests BBD18 function is essential in mammalian hosts but redundant in the arthropod vector. Notably, although bbd18 expression and in vitro growth defects are restored in the complemented isolates, their phenotype is similar to the mutants - being unable to persist in mice but able to survive in ticks. Despite low expression in cultured wild-type B. burgdorferi, bbd18 deletion downregulated several genes. Interestingly, expression of some, including ospD and bbi39, could be complemented, while that of others could not be restored via bbd18 re-expression. Correspondingly, bbd18 mutants displayed altered production of several proteins, and similar to RNA levels, some were restored in the bbd18 complement and others not. To understand how bbd18 deletion results in apparently permanent and noncomplementable phenotypic defects, we sought to genetically disturb the DNA topology surrounding the bbd18 locus without deleting the gene. Spirochetes with an antibiotic cassette inserted downstream of the gene, between bbd17 and bbd18, were significantly attenuated in mice, while a similar upstream insertion, between bbd18 and bbd19, did not affect infectivity, suggesting that an unidentified cis element downstream of bbd18 may encode a virulence-associated factor critical for infection.

Formulation and characterization of a 0.1% rapamycin cream for the treatment of Tuberous Sclerosis Complex-related angiofibromas

International audience

Influence of magnesium on biochemical parameters of iron and oxidative stress in patients with type 2 diabetes

Introduction: Studies have shown that oxidative stress, found in patients with type 2 diabetes, may be due to changes in the metabolism of minerals, such as magnesium and iron. Data related to compartmentalization of these minerals in diabetes are scarce and controversial. Objective: This study assessed the influence of magnesium on biochemical parameters of iron and oxidative stress in patients with type 2 diabetes. Methods: A case-control study in male and female subjects aged 27-59 years, divided into two groups: type 2 diabetes (n=40) and control (n=48). Intake of magnesium and iron was assessed by three-day food record. Plasma, erythrocyte and urinary levels of magnesium, serum iron, ferritin, total iron binding capacity, fasting glucose, glycated hemoglobin, insulin, creatinine clearance and plasma thiobarbituric acid reactive substances (TBARS) were analyzed. Results and Discussion: Magnesium intake and plasma magnesium were lower in diabetic subjects. There was low urinary magnesium excretion, with no difference between groups. Although normal, the diabetic group had lower serum iron and ferritin concentrations compared to control subjects. Plasma TBARS in diabetic patients was higher than control while creatinine clearance was lower. An inverse correlation between erythrocyte magnesium and serum iron and ferritin was observed in the diabetes group. Conclusions: Diabetes induced hypomagnesemia and this, associated with chronic hyperglycemia, may have enhanced oxidative stress. Erythrocyte magnesium may have contributed to prevent iron overload and worsening of oxidative stress and hyperglycemic status.

Structural Aspects of the Distinct Biochemical Properties of Glutaredoxin 1 and Glutaredoxin 2 from Saccharomyces cerevisiae

Glutaredoxins (Grxs) are small (9-12 kDa) heat-stable proteins that are ubiquitously distributed. In Saccharomyces cerevisiae, seven Grx enzymes have been identified. Two of them (yGrx1 and yGrx2) are dithiolic, possessing a conserved Cys-Pro-Tyr-Cys motif. Here, we show that yGrx2 has a specific activity 15 times higher than that of yGrx1, although these two oxidoreductases share 64% identity and 85% similarity with respect to their amino acid sequences. Further characterization of the enzymatic activities through two-substrate kinetics analysis revealed that yGrx2 possesses a lower Km for glutathione and a higher turnover than yGrx1. To better comprehend these biochemical differences, the pK(a) of the N-terminal active-site cysteines (Cys27) of these two proteins and of the yGrx2-C30S mutant were determined. Since the pK(a) values of the yGrx1 and yGix2 Cys27 residues are very similar, these parameters cannot account for the difference observed between their specific activities. Therefore, crystal structures of yGrx2 in the oxidized form and with a glutathionyl mixed disulfide were determined at resolutions of 2.05 and 1.91 angstrom, respectively. Comparisons of yGrx2 structures with the recently determined structures of yGrx1 provided insights into their remarkable functional divergence. We hypothesize that the substitutions of Ser23 and Gln52 in yGrx1 by Ala23 and Glu52 in yGrx2 modify the capability of the active-site C-terminal cysteine to attack the mixed disulfide between the N-terminal active-site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between yGrx1 and yGrx2 may reflect variations in substrate specificity. (C) 2008 Elsevier Ltd. All rights reserved.

MEMS SENSOR PLATFORMS FOR IN SITU CHARACTERIZATION OF LI-ION BATTERY ELECTRODES

Lithium-ion batteries provide high energy density while being compact and light-weight and are the most pervasive energy storage technology powering portable electronic devices such as smartphones, laptops, and tablet PCs. Considerable efforts have been made to develop new electrode materials with ever higher capacity, while being able to maintain long cycle life. A key challenge in those efforts has been characterizing and understanding these materials during battery operation. While it is generally accepted that the repeated strain/stress cycles play a role in long-term battery degradation, the detailed mechanisms creating these mechanical effects and the damage they create still remain unclear. Therefore, development of techniques which are capable of capturing in real time the microstructural changes and the associated stress during operation are crucial for unravelling lithium-ion battery degradation mechanisms and further improving lithium-ion battery performance. This dissertation presents the development of two microelectromechanical systems sensor platforms for in situ characterization of stress and microstructural changes in thin film lithium-ion battery electrodes, which can be leveraged as a characterization platform for advancing battery performance. First, a Fabry-Perot microelectromechanical systems sensor based in situ characterization platform is developed which allows simultaneous measurement of microstructural changes using Raman spectroscopy in parallel with qualitative stress changes via optical interferometry. Evolutions in the microstructure creating a Raman shift from 145 cm−1 to 154 cm−1 and stress in the various crystal phases in the LixV2O5 system are observed, including both reversible and irreversible phase transitions. Also, a unique way of controlling electrochemically-driven stress and stress gradient in lithium-ion battery electrodes is demonstrated using the Fabry-Perot microelectromechanical systems sensor integrated with an optical measurement setup. By stacking alternately stressed layers, the average stress in the stacked electrode is greatly reduced by 75% compared to an unmodified electrode. After 2,000 discharge-charge cycles, the stacked electrodes retain only 83% of their maximum capacity while unmodified electrodes retain 91%, illuminating the importance of the stress gradient within the electrode. Second, a buckled membrane microelectromechanical systems sensor is developed to enable in situ characterization of quantitative stress and microstructure evolutions in a V2O5 lithium-ion battery cathode by integrating atomic force microscopy and Raman spectroscopy. Using dual-mode measurements in the voltage range of the voltage range of 2.8V – 3.5V, both the induced stress (~ 40 MPa) and Raman intensity changes due to lithium cycling are observed. Upon lithium insertion, tensile stress in the V2O5 increases gradually until the α- to ε-phase and ε- to δ-phase transitions occur. The Raman intensity change at 148 cm−1 shows that the level of disorder increases during lithium insertion and progressively recovers the V2O5 lattice during lithium extraction. Results are in good agreement with the expected mechanical behavior and disorder change in V2O5, highlighting the potential of microelectromechanical systems as enabling tools for advanced scientific investigations. The work presented here will be eventually utilized for optimization of thin film battery electrode performance by achieving fundamental understanding of how stress and microstructural changes are correlated, which will also provide valuable insight into a battery performance degradation mechanism.

Integrative genomic, epigenetic and metabolomic characterization of beef from grass-fed Angus steers

Beef constitutes a main component of the American diet and still represent the principal source of protein in many parts of the world. Currently, the meat market is experiencing an important transformation; consumers are increasingly switching from consuming traditional beef to grass-fed beef. People recognized products obtained from grass-fed animals as more natural and healthy. However, the true variations between these two production systems regarding various aspects remain unclear. This dissertation provides information from closely genetically related animals, in order to decrease confounding factors, to explain several confused divergences between grain-fed and grass-fed beef. First, we examined the growth curve, important economic traits and quality carcass characteristics over four consecutive years in grain-fed and grass-fed animals, generating valuable information for management decisions and economic evaluation for grass-fed cattle operations. Second, we performed the first integrated transcriptomic and metabolomic analysis in grass-fed beef, detecting alterations in glucose metabolism, divergences in free fatty acids and carnitine conjugated lipid levels, and altered β-oxidation. Results suggest that grass finished beef could possibly benefit consumer health from having lower total fat content and better lipid profile than grain-fed beef. Regarding animal welfare, grass-fed animals may experience less stress than grain-fed individuals as well. Finally, we contrasted the genome-wide DNA methylation of grass-fed beef against grain-fed beef using the methyl-CpG binding domain sequencing (MBD-Seq) method, identifying 60 differentially methylated regions (DMRs). Most of DMRs were located inside or upstream of genes and displayed increased levels of methylation in grass-fed individuals, implying a global DNA methylation increment in this group. Interestingly, chromosome 14, which has been associated with large effects on ADG, marbling, back fat, ribeye area and hot carcass weight in beef cattle, allocated the largest number of DMRs (12/60). The pathway analysis identified skeletal and muscular system as the preeminent physiological system and function, and recognized carbohydrates metabolism, lipid metabolism and tissue morphology among the highest ranked networks. Therefore, although we recognize some limitations and assume that additional examination is still required, this project provides the first integrative genomic, epigenetic and metabolomics characterization of beef produced under grass-fed regimen.

Characterization of silver nanoparticles prepared by wet chemical method and their antibacterial and cytotoxicity activities

Purpose: To investigate the efficiency of silver nanoparticles synthesized by wet chemical method, and evaluate their antibacterial and anti-cancer activities. Methods: Wet chemical method was used to synthesize silver nanoparticles (AgNPs) from silver nitrate, trisodium citrate dehydrate (C6H5O7Na3.2H2O) and sodium borohydride (NaBH4) as reducing agent. The AgNPs and the reaction process were characterized by UV–visible spectrometry, zetasizer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) equipped with energy dispersive spectroscopy (EDS). The antibacterial and cytotoxic effects of the synthesized nanoparticles were investigated by agar diffusion method and MTT assay respectively. Results: The silver nanoparticles formed were spherical in shape with mean size of 10.3 nm. The results showed good antibacterial properties, killing both Gram-positive and Gram-negative bacteria, and its aqueous suspension displayed cytotoxic activity against colon adenocarcinoma (HCT-116) cell line. Conclusion: The findings indicate that silver nanoparticles synthesized by wet chemical method demonstrate good cytotoxic activity in colon adenocarcinoma (HCT-116) cell lines and strong antibacterial activity against various strains of bacteria.