ucalgary_2015_bahafzallah_laila.pdf

UNIVERSITY OF CALGARY
Quantification of HIV-1 Proviral DNA Forms in Gut Tissues Using Real-Time PCR
by
Laila Bahafzallah
A THESIS
SUBMITTED TO THE FACULTY OF GRADUATE STUDIES
IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE
DEGREE OF MASTER OF SCIENCE
GRADUATE PROGRAM IN MICROBIOLOGY AND INFECTIOUS DISEASES
CALGARY, ALBERTA
SEPTEMBER, 2015
© Laila Bahafzallah 2015

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Abstract
Previous studies have shown that infection of gut tissues (esophagus-stomach-duodenum-
colon) by HIV is compartmentalized with increased HIV-1 diversity and selection for drug
resistance in the colon. We looked at the kinetics of HIV-1 in the gut tissues obtained from
infected patients receiving ART (i.e AZT or ddI). We established real- time PCR protocols to
detect HIV-1 proviral DNA forms. The total HIV-1 proviral DNA was the most frequent form
found in the gut tissues. 2-LTR proviral DNA was also detected but in low levels which might
indicate low viral replication. HIV-1 latent infection was also detected in the gut tissues as
represented by the integrated proviral DNA levels. The levels detected of the proviral DNA
forms varied between gut tissues, visits and patients, and no difference or correlation were found
for patients receiving AZT or ddI.

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Acknowledgments
My journey to get this degree was faced with many challenges, however, I met amazing
people who did not give up on me and always encouraged me to thrive for excellent. I could not
have completed this degree without them. First, I would like to thank Allah for blessing me
everyday. I also would like to thank my mentor and my supervisor Dr. Guido van Marle for
giving the opportunity to be in his lab and for his constant support throughout my degree. I
would never be at this point in my journey without his help and guidance. I am also grateful for
my committee members for their advice and suggestions for my research. Dr. Glen Armstrong it
was honor to have a great scientist like you in my committee and l am truly thankful for
everything you have done for me. Dr. Carla Coffin thank you for the continuous support and
encouragement. Dr. Markus Czub thank you for all your advice and insights. Dr. Careem thank
you for your time and help.
I would like to give a special thanks to Dr. Michael Eschbaumer for his generous sharing of
his real time PCR expertise. I also would like to thank our lab technician Sandi Nishikawa for
saving the day and make things right. I also thank Dr. Wendy Hutchins for her continous support
and generous advice. She has been a great teacher that I always look up to.
I would like to acknowledge the department of Microbiology and Infectious Diseases
Graduate program, Snyder Institute for Chronic Diseases and the ministry of higher education in
Saudi Arabia for the funding. A special thanks goes to our late King Abdulla may he rest in
peace. I also acknowledge Dr. Ali Al-Beshri for his help. I give my great appreciation to my
academic advisor Dr. Ahmad Ismail who always been generous with his time and advice through
my entire journey.

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I would like to thank our Virology group with all the students and investigators as I am so
grateful to be a part of that joyful group.
Finally, I want to thank my family and friends who put up with all my drama and draw a
smile on my face. I am grateful for your love and support.

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I dedicate this thesis to my all my family, especially my Mom, Dad, my
sisters Lamis and Lama, my brother Louay, Aunt Lolly and uncle
Mohammed-Ali, uncle Mohammed-Noor and last but not least for my
beautiful daughter Sara.