Development of techniques for testing the effect of the E1 region on adenovirus integration /

Adenoviral vectors are currently the most widely used gene therapeutic vectors, but their inability to integrate into host chromosomal DNA shortened their transgene expression and limited their use in clinical trials. In this project, we initially planned to develop a technique to test the effect of the early region 1 (E1) on adenovirus integration by comparing the integration efficiencies between an E1-deleted adenoviral vector (SubE1) and an Elcontaining vector (SubE3). However, we did not harvest any SubE3 virus, even if we repeated the transfection and successfully rescued the SubE1 virus (2/4 transfections generated viruses) and positive control virus (6/6). The failure of rescuing SubE3 could be caused by the instability of the genomic plasmid pFG173, as it had frequent intemal deletions when we were purifying It. Therefore, we developed techniques to test the effect of E1 on homologous recombination (HR) since literature suggested that adenovirus integration is initiated by HR. We attempted to silence the E1 in 293 cells by transfecting E1A/B-specific small interfering RNA (siRNA). However, no silenced phenotype was observed, even if we varied the concentrations of E1A/B siRNA (from 30 nM to 270 nM) and checked the silencing effects at different time points (48, 72, 96 h). One possible explanation would be that the E1A/B siRNA sequences are not potent enough to Induce the silenced phenotype. For evaluating HR efficiencies, an HR assay system based on bacterial transfonmatJon was designed. We constmcted two plasmids ( designated as pUC19-dl1 and pUC19-dl2) containing different defective lacZa cassettes (forming white colonies after transformation) that can generate a functional lacZa cassette (forming blue colonies) through HR after transfecting into 293 cells. The HR efficiencies would be expressed as the percentages of the blue colonies among all the colonies. Unfortunately, after transfonnation of plasmid isolated from 293 cells, no colony was found, even at a transformation efficiency of 1.8x10^ colonies/pg pUC19, suggesting the sensitivity of this system was low. To enhance the sensitivity, PCR was used. We designed a set of primers that can only amplify the recombinant plasmid fomied through HR. Therefore, the HR efficiencies among different treatments can be evaluated by the amplification results, and this system could be used to test the effect of E1 region on adenovirus integration. In addition, to our knowledge there was no previous studies using PCR/ Realtime PCR to evaluate HR efficiency, so this system also provides a PCR-based method to carry out the HR assays.

Gas chromatographic electron capture negative ionization mass spectrometric (GC/ECNI/MS) determination of unique fluorinated compounds in the sediments of Lake Ontario and the effect of high-boiling alcohols (as injection solvents) on chromatographic behaviour of polycyclic aromatic hydrocarbons in gas chromatography

Part I - Fluorinated Compounds A method has been developed for the extraction, concentration, and determination of two unique fluorinated compounds from the sediments of Lake Ontario. These compounds originated from a common industrial landfill, and have been carried to Lake Ontario by the Niagara River. Sediment samples from the Mississauga basin of Lake Ontario have been evaluated for these compounds and a depositional trend was established. The sediments were extracted by accelerated solvent extraction (ASE) and then underwent clean-up, fractionation, solvent exchange, and were concentrated by reduction under nitrogen gas. The concentrated extracts were analyzed by gas chromatography - electron capture negative ionization - mass spectrometry. The depositional profile determined here is reflective of the operation of the landfill and shows that these compounds are still found at concentrations well above background levels. These increased levels have been attributed to physical disturbances of previously deposited contaminated sediments, and probable continued leaching from the dumpsite. Part II - Polycyclic Aromatic Hydrocarbons Gas chromatography/mass spectrometry is the most common method for the determination of polycyclic aromatic hydrocarbons (PAHs) from various matrices. Mass discrimination of high-boiling compounds in gas chromatographic methods is well known. The use of high-boiling injection solvents shows substantial increase in the response of late-eluting peaks. These solvents have an increased efficiently in the transfer of solutes from the injector to the analytical column. The effect of I-butanol, I-pentanol, cyclopentanol, I-hexanol, toluene and n-octane, as injection solvents, was studied. Higher-boiling solvents yield increased response for all PAHs. I -Hexanol is the best solvent, in terms of P AH response, but in this solvent P AHs were more susceptible to chromatographic problems such as peak splitting and tailing. Toluene was found to be the most forgiving solvent in terms of peak symmetry and response. It offered the smallest discrepancies in response, and symmetry over a wide range of initial column temperatures.

X-ray diffraction of a gram-negative bacterial membrane mimetic

This thesis applies x-ray diffraction to measure he membrane structure of lipopolysaccharides and to develop a better model of a LPS bacterial melilbrane that can be used for biophysical research on antibiotics that attack cell membranes. \iVe ha'e Inodified the Physics department x-ray machine for use 3.'3 a thin film diffractometer, and have lesigned a new temperature and relative humidity controlled sample cell.\Ve tested the sample eel: by measuring the one-dimensional electron density profiles of bilayers of pope with 0%, 1%, 1G :VcJ, and 100% by weight lipo-polysaccharide from Pse'udo'lTwna aeTuginosa. Background VVe now know that traditional p,ntibiotics ,I,re losing their effectiveness against ever-evolving bacteria. This is because traditional antibiotic: work against specific targets within the bacterial cell, and with genetic mutations over time, themtibiotic no longer works. One possible solution are antimicrobial peptides. These are short proteins that are part of the immune systems of many animals, and some of them attack bacteria directly at the membrane of the cell, causing the bacterium to rupture and die. Since the membranes of most bacteria share common structural features, and these featuret, are unlikely to evolve very much, these peptides should effectively kill many types of bacteria wi Lhout much evolved resistance. But why do these peptides kill bacterial cel: '3 , but not the cells of the host animal? For gramnegative bacteria, the most likely reason is that t Ileir outer membrane is made of lipopolysaccharides (LPS), which is very different from an animal :;ell membrane. Up to now, what we knovv about how these peptides work was likely done with r !10spholipid models of animal cell membranes, and not with the more complex lipopolysa,echaricies, If we want to make better pepticies, ones that we can use to fight all types of infection, we need a more accurate molecular picture of how they \vork. This will hopefully be one step forward to the ( esign of better treatments for bacterial infections.

Subliminal Exposure to Empathy Primes: A New Method to Reduce Intergroup Bias?

An abundant literature has demonstrated the benefits of empathy for intergroup relations (e.g., Batson, Chang, Orr, & Rowland, 2002). In addition, empathy has been identified as the mechanism by which various successful prejudice-reduction procedures impact attitudes and behaviour (e.g., Costello & Hodson, 2010). However, standard explicit techniques used in empathy-prejudice research have a number of potential limitations (e.g., resistance; McGregor, 1993). The present project explored an alternative technique, subliminally priming (i.e., outside of awareness) empathy-relevant terms (Study 1), or empathy itself (Study 2). Study 1 compared the effects of exposure to subliminal empathy-relevant primes (e.g., compassion) versus no priming and priming the opposite of empathy (e.g., indifference) on prejudice (i.e., negative attitudes), discrimination (i.e., resource allocation), and helping behaviour (i.e., willingness to empower, directly assist, or expect group change) towards immigrants. Relative to priming the opposite of empathy, participants exposed to primes of empathy-relevant constructs expressed less prejudice and were more willingness to empower immigrants. In addition, the effects were not moderated by individual differences in prejudice-relevant variables (i.e., Disgust Sensitivity, Intergroup Disgust-Sensitivity, Intergroup Anxiety, Social Dominance Orientation, Right-wing Authoritarianism). Study 2 considered a different target category (i.e., Blacks) and attempted to strengthen the effects found by comparing the impact of subliminal empathy primes (relative to no prime or subliminal primes of empathy paired with Blacks) on explicit prejudice towards marginalized groups and Blacks, willingness to help marginalized groups and Blacks, as well as implicit prejudice towards Blacks. In addition, Study 2 considered potential mechanisms for the predicted effects; specifically, general empathy, affective empathy towards Blacks, cognitive empathy towards Blacks, positive mood, and negative mood. Unfortunately, using subliminal empathy primes “backfired”, such that exposure to subliminal empathy primes (relative to no prime) heightened prejudice towards marginalized groups and Blacks, and led to stronger expectations that marginalized groups and Blacks improve their own situation. However, exposure to subliminal primes pairing empathy with Blacks (relative to subliminal empathy primes alone) resulted in less prejudice towards marginalized groups and more willingness to directly assist Blacks, as expected. Interestingly, exposure to subliminal primes of empathy paired with Blacks (vs. empathy alone) resulted in more pro-White bias on the implicit prejudice measure. Study 2 did not find that the potential mediators measured explained the effects found. Overall, the results of the present project do not provide strong support for the use of subliminal empathy primes for improving intergroup relations. In fact, the results of Study 2 suggest that the use of subliminal empathy primes may even backfire. The implications for intergroup research on empathy and priming procedures generally are discussed.