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Detection of Aerobic Bacterial Endospores: from Air Sampling, Sterilization Validation to Astrobiology

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Detection of Aerobic Bacterial Endospores: from Air Sampling, Sterilization Validation to Astrobiology DETECTION OF AEROBIC BACTERIAL ENDOSPORES: FROM AIR SAMPLING, STERILIZATION VALIDATION TO ASTROBIOLOGY Thesis by Pun To (Douglas) Yung In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2008 (Defended May 9, 2008) ii © 2008 Pun To (Douglas) Yung All Rights Reserved iii Acknowledgment I would like to express my deepest gratitude to my thesis adviser, Dr. Adrian Ponce, for his guidance and support. It is due to his scholastic guidance and encouragement that ultimately made this work possible. I appreciate the time and attention of my committee members: Professor Morteza Gharib, Professor Scott Fraser, and Professor Changhuei Yang. Given their busy schedules, it has been kind of them to play a role in my course of study. I owe my gratitude to all members of the Ponce Group who have made this dissertation possible, and because of them my graduate experience has been one that I will cherish forever. Elizabeth Lester has kindly introduced me to techniques in microbiology. Alan Fung has taught me principles in mechanical engineering and instrument design. I have enjoyed working with Elizabeth Lester, Alan Fung, Morgan Cable, Hannah Shafaat and Wanwan Yang. I would like express thanks to my summer undergraduate mentees, Wilson Sung, Christine Tarleton, and William Fan, who have contributed important pieces to my thesis work. I would like to acknowledge the other individuals who have contributed to the completion of this thesis: Dr. James Kirby, Dr. Xenia Amashukeli, Dr. Christine Pelletier, Raymond Lam, Dr. Michael Kempf, Michael Lee, Dr. Fei Chen, Dr. Anita Fisher, Dr. Steve Monacos, Dr. Stephanie Connon, and Dr. Donald Obenhuber. I appreciate the support from the many reliable staff members working at JPL and Caltech, including Stacey Klinger, Robert Downer, Icy Ma, Steve Gould, Lillian Kremar, Joe Drew, Cora Carriedo, and Carlos Hernandez. Last but not least, I have to thank Linda Scott for being the most efficient professional in bioengineering. I would like to thank iv Ray Pini, Amir Ettehdieh and Universal Detection Technology for helpful discussions. I thank Fei Chen for her help in a preliminary vaporized hydrogen peroxide experiment and access to the spacecraft assembly clean room. I thank Steris Corporation for preparing vaporized hydrogen peroxide treated-endospore strips. I am also indebted to my friends and family for their continuous support, love and patience. Particularly, I would like to express my heartfelt gratitude to Jerry Ruiz and Karen Chan. I warmly appreciate the encouragement from Dr. Stephen Shum and Dr. James Tong from high school, college, to graduate school. v “The most beautiful and most profound emotion we can experience is the sensation of the mystical. It is the source of all true science. He to whom the emotion is a stranger, who can no longer wonder and stand rapt in awe, is as good as dead.” Albert Einstein vi Abstract Bacterial endospores are formed in genera such as Bacillus and Clostridium in times of incipient stresses. Derivative of their remarkable resistance and ubiquity, endospores are delivery vehicles for anthrax attack, biological indicators for checking sterilization efficacy, and candidates for Panspermia and potential extraterrestrial life, thereby underscoring the significance of their rapid detection. In this thesis project, spectroscopy and microscopy methods are studied to measure the release of a unique constituent, dipicolinic acid (DPA), via germination as a proxy for endospore viability. In particular, a luminescence time-gated microscopy technique (called microscopy endospore viability assay, acronym: µEVA) has been developed to enumerate germination-capable aerobic endospores rapidly based on energy transfer from DPA to terbium ions doped on a solid matrix upon UV excitation. The distinctive emission and millisecond lifetime enable time-resolved imaging to achieve a sensitivity of one endospore. Effective air sampling of endospores is crucial in view of the potential catastrophe caused by the dissemination of airborne anthrax endospores. Based on time-gated spectroscopy of terbium-DPA luminescence, the Anthrax Smoke Detector has been built to provide real-time surveillance of air quality for timely mitigation and decontamination. This technology also finds application in the monitoring of airborne endospore bioburden as an indicator of total biomass in a closed spacecraft system in order to safeguard the health of astronauts. Sterilization validation is of prime concern in the medical field and planetary protection to prevent cross-contaminations among patients and planets. µEVA has yielded faster and comparable results compared with the culture-based NASA standard assay in vii assessing surface endospore bioburden on spacecraft materials and clean rooms surfaces. The current analysis time has been expedited from 3 days to within an hour in compliance with planetary protection requirements imposed on landers and probes designed for life detection missions. From the perspective of astrobiology, endospores are time capsules preserving geological history and may exist as dormant lives in analogous extraterrestrial environments. µEVA has successfully recovered ancient endospores in cold biospheres (Greenland ice core, Antarctic Lake Vida, polar permafrost) and hyper-arid biospheres (Atacama Desert) on Earth as templates for determining life longevity and the search of extinct or extant life on Mars and other icy celestial bodies. Result authenticity has been validated by a comprehensive suite of experiments encompassing culture-based and culture-independent techniques such as epifluorescence microscopy, flow cytometry, fluorometry, bioluminescence and 16s rRNA analysis. In conclusion, µEVA is a sensitive analytical tool that opens a new realm in microbiology to provide insights into air sampling, sterility assessment and exobiology. viii Table of contents ACKNOWLEDGMENT………………………………………………………………………………………iii ABSTRACT ..................................................................................................................................................vi TABLE OF CONTENTS ............................................................................................................................... viii LIST OF FIGURES ........................................................................................................................................ xv LIST OF TABLES ...................................................................................................................................... xviii CHAPTER 1: INTRODUCTION ....................................................................................... 1 1.1 INTRODUCTION ...................................................................................................................................... 1 1.2 LIFE CYCLE OF AN SPORE-FORMING BACTERIA ....................................................................................... 5 1.3 DPA-TRIGGERED TERBIUM PHOTOLUMINESCENCE ASSAY ...................................................................... 7 1.4 OUTLINE OF THESIS .............................................................................................................................. 10 1.5 REFERENCES ........................................................................................................................................ 16 CHAPTER 2: REVIEW OF ENDOSPORE DETECTION TECHNOLOGY ................. 21 2.1 ABSTRACT ........................................................................................................................................... 21 2.2 INTRODUCTION .................................................................................................................................... 21 2.3 BIOMARKER METHODS ......................................................................................................................... 24 2.3.1 Calcium dipicolinate ................................................................................................................... 25 2.3.2 Dipicolinic acid ........................................................................................................................... 27 2.3.3 DNA ............................................................................................................................................. 31 2.4 OPTICAL PROPERTY AND STAINABILITY ............................................................................................... 34 2.4.1 Direct epifluorescent filtration technique .................................................................................... 34 2.4.2 Coulter counter ........................................................................................................................... 35 2.4.3 Method of Schaeffer and Fulton .................................................................................................. 35 2.4.4 Phase contrast microscopy .......................................................................................................... 36 2.4.5 Electron microscopy .................................................................................................................... 38 2.4.6 Flow cytometry ............................................................................................................................ 38 2.5 METABOLISM ......................................................................................................................................
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