Research Group Members

Jeanine P. Wiener-Kronish is a Professor of Anesthesia and Medicine and Vice-Chairman of the Department of Anesthesia and Perioperative Care. Dr. Wiener-Kronish obtained her BA from the University of California at Los Angeles in 1971 and then obtained her M.D. in 1976 from the University of California at San Francisco. She completed her residency in Internal Medicine in 1979 and a Pulmonary clinical and research fellowship at the Cardiovascular Research Institute (UCSF) in 1984. She then completed a residency in Anesthesia (UCSF) in 1986. She is board certified in Internal Medicine, Pulmonary, Anesthesia and Critical Care Medicine. She obtained tenure at UCSF in 1992 and became a professor in 1996.

Dr. Wiener-Kronish has received awards for her scholarship, including Phi Beta Kappa, Phi Gamma Mu and Mortar Board. She was awarded the Outstanding Woman House Officer award for her work as a resident in Internal Medicine. She then won the Stuart Cullen Award for Excellence in Clinical Anesthesia for her work as an Anesthesia Resident. She has been elected to the Institute of Medicine, Cardiovascular Research Institute, the Western Society for Clinical Research, the American Physiological Society, the Association of University Anesthesiologists, and the Western Association of Physicians. She was chosen for the Program in Executive Leadership in Academic Medicine, a training program for academic women and for the training program for Chairs and Deans by the AAMC. She was chosen to be the Foundation of Anesthesia Researcher Speaker in October 2003 at the national meeting of the American Society of Anesthesiologists and to present the plenary lecture at the Association of University Anesthesiologists.

Dr. Judith Flanagan received her BS (Hons) from University of Sydney, Australia and after spending 3 years working on the Human Genome Project, (LBNL, California) returned to Australia to obtain a PhD in Medicine from the University of New South Wales. An unusual segue during her postdoctoral studies at UC Berkeley into environmental science to study the genetics of a microbial acid mine drainage community combined with her medical research background culminated in her present appointment in TRMP studying the "ecology" of patients infected and colonized by communities of pathogens whose effect on the patient is as much a dynamic of the microbial community interactions as that of the human/pathogen. Her present research pursuits include 16s rRNA analysis of microbial communities to determine the culturable and non-culturable organisms infecting patients with ventillator acquired pneumonia (VAP), asthma, cystic fibrosis and chronic suppurative otitis media (CSOM) a disease leading to hearing loss in children in marginalized communities. Understanding the ecology of human bacterial infections will potentially aid in more effective antibiotic treatment and alternative personalized therapies.

Dr. Lynch received her undergraduate degree from University College Dublin, Ireland majoring in Industrial Microbiology with minors in Chemistry and Biostatistics. She remained in the Department to complete her graduate studies under the supervision of Dr. Patrick Caffrey, where she was involved in identification and characterization of the gene cluster responsible for biosynthesis of the polyketide antifungal, Amphotericin B. Following postdoctoral work with Professor Paul C. Engel characterizing a glutamine dehydrogenase of a marine psychrophile, Susan moved to California to work with Dr. A.C. Matin at Stanford University. There she examined various aspects of bacterial physiology, including microbial chromate bioremediation, improvement of anti-cancer prodrug therapy, the effect of low shear simulated microgravity on Escherichia coli stress response regulation and biofilm physiology, and the molecular basis of antimicrobial resistance of uropathogenic E. coli biofilms.

In June 2005, Susan joined the Translational Research on Microbial Pathogens group at UCSF. Dr. Lynch's primary research focus is biofilm formation and virulence gene expression of the respiratory pathogen Pseudomonas aeruginosa from both Cystic Fibrosis (CF) and ICU patients. Dr. Lynch's research aims to provide a better understanding of the response of this versatile microorganism in a clinical setting, improve diagnosis and provide efficacious strain-specific combinatorial therapeutic options to improve patient outcome.

Dr. Martin Allgaier completed his PhD at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany, in 2006, submitting the thesis, "Diversity and Dynamics of Bacterioplankton communities in four selected lakes of the Mecklenburg Lake District". He joined the Translational Research on Microbial Pathogens group in February 2007, bringing with him experiences in microbial ecology particularly in analyzing complex bacterial communities. His current research focuses on study phylogenetic and functional diversity of bacterial communities in patients with cystic fibrosis (CF), ventilator acquired pneumoniae (VAP), and asthma. His research aims to provide a better understanding of the response of complete bacterial communities to acute microbial infections and will potentially improve diagnostics and therapy of such infections.

Seung graduated from UC Berkeley with a B.A. in Molecular Cell and Biology in 2004 and joined the group in July of 2005. Previous to joining the the group here in UCSF, Seung worked with a group in Berkeley that studied community dynamics of microbes in uranium contaminated soils. Here, he assists the Principal Investigator with sample preparation, DNA extraction, RNA preparation, PCR, real-time PCR, Western Blots, pulse-field determinations, RAPD measurements, microarray analysis, and other duties as assigned.

I have been working at UCSF for more than 20 years with the Cardiovascular Research Institute and the Dept of Anesthesia in studies involving both basic science and clinical research. I have been working with the Translational Research on Microbial Pathogens group since October of 2003. I collect data from adult and Pediatric/Neonatal ICU patients who are found to have infections of Pseudomonas during their stay in the ICU. The information in the Access database will allow correlation between Pseudomonas strains and virulence factors and clinical condition and outcomes.

Dave Kilough joined the Anesthesia Laboratory in 2006 and provides operational support to Dr. Wiener-Kronish and five other Principal Investigators. Before coming to UCSF he worked as a planning analyst for Children’s Hospital Oakland and in strategy and business development for Sutter Health. He has a BA in International Relations, World Trade and Development from UC-Davis, frequent volunteer gigs with local classical music performances, and a dog named Gir.

Fenny Kuo has experience in a variety of industries. She has provided support for microchip design groups at Intel Corp., conducted outreach and analysis for community development, supported the editorial department of a weekly newspaper, coordinated photo shoots for a clothing company, and managed a small CD-ROM development project. Outside of work, she has been involved in volunteer activities including producing fundraisers, coordinating volunteers for arts organizations, and most recently working with grassroots relief organizations in New Orleans.

Rachel Dotson is a clinical and research fellow in the Division of Pulmonary and Critical Care Medicine. Rachel received a B.A. from the University of Texas at Austin in 1994 and her M.D. from U.T. Southwestern Medical Center at Dallas in 1998. She completed her internship and residency training in Internal Medicine at Vanderbilt University Medical Center, where she also served as the Hugh J. Morgan Chief Medical Resident from 2001-2002. Her research interests include the utilization of PCR-based methods and biomarkers of lung injury in the diagnosis of ventilator-associated pneumonia. She is also applying these diagnostic tools in a longitudinal study of lung transplant recipients to detect acute and chronic transplant rejection and infection.

I obtained my M.D. in 1984 at the Universidad Autonoma Benito Juarez de Oaxaca, Mexico. After graduating in 1984, I defected from Nicaragua to the United States. In 1986, I began to pursue a career in Respiratory Therapy. I attended Skyline College in San Bruno, CA and graduated in 1989 as a Respiratory Care Practitioner. I began working at UCSF as a Respiratory Therapist in December of 1989. Six months later I became a Registered Respiratory Therapist by completing the California Board Examination of Respiratory Care. In 2004, I became a RRT II (Clinical Coordinator). Over the years, aside from working clinically in the intensive care units I have participated in various research studies sponsored by the NIH. These studies included: LaSRS (steroids vs. Placebo in patients with ARDS), Ketokonazole vs. Placebo, Lysophilline vs. Placebo, ARDS Net Protocol, high PEEP vs. low PEEP in patients with ARDS, Dead Space Studies, FACTT (fluid assesment catheter therapy trial) headed by the P.I. Dr. Michael Matthay. Currently I work for the VAP (Ventilator Associated Pneumonia) study directed by Dr. Jeanine Wiener-Kronish. I started working for the VAP Study in 2003. In all of these studies, my tasks included screening patients, obtaining consents, and gathering data from the patients enrolled in the study. However, most importantly for the VAP study I helped implement the mini-BAL Standard Protocol in the intensive care units as a tool for diagnosing VAP.

Amua Rubio-Mills received her BS in Physiology from San Francisco State University in 2004. She joined the Translational Research Group on Microbial Pathogens at UCSF in July 2005, where she has assisted in identifying clinical isolates of Psuedomonas aeruginosa, as well as differentiating between colonized and infected patients in the ICU. In addition, she has assisted in characterizing P. aeruginosa through the use of Real Time, Rapid and multiplex PCR.

Yoriko Sawa was a registered nurse in Anesthesiology, Radiology, Oral surgery, in the Newborn Intensive Care Unit in Kyoto University, Japan, from 1985 to 1989. She moved to San Francisco eleven years ago and started working with the Translational Research Group on Microbial Pathogens last summer.

Gaurav Singh graduated from UC Berkeley with a BA in Molecular and Cell Biology in 2002. He is currently a fourth year medical student at UCSF. Gaurav joined the group for a summer in 2003. He has returned for a full year of research from June 2006 to June 2007 under the Pathways to Careers in Clinical and Translational Research (PACCTR) Program. Gaurav’s prior research experiences include investigating mechanisms of membrane fusion in gastric parietal cells (John Forte’s lab at UC Berkeley) and the pathogenesis and treatment of mycoses in murine models (David Stevens’ lab at Santa Clara Valley Medical Center). In the summer of 2003, Gaurav studied the associations between bacterial burdens of Pseudomonas aeruginosa in ventilator associated pneumonia and clinical outcomes in patients. He is currently working on elucidating mechanisms of pathogenesis for Pseudomonas as well as utilizing a universal 16s microarray to characterize bacterial infections in hospitalized patients, with a focus on bacteremia.

Dr. Yuanlin Song received his M.D. degree in 1994 and Master's Degree in 1996 at Shanghai Medical University (now the medical college of Fudan University, Shanghai). After graduation, he became a resident in the department of Pulmonary Medicine, Zhongshan Hospital. He joined the labs of Drs. Alan S. Verkman and Michael A. Matthay at the Cardiovascular Research Institute, University of California, San Francisco in 1998 as a postdoctoral fellow. His major research areas were (1) aquaporin water channel and lung fluid transport, and (2) cystic fibrosis airway disease and submucosal gland secretion. Dr. Song uses epi-fluorescence microscopy and dual wavelength ratiometric fluorescence techniques to quantify ion and water transport as well as ion concentration in airway surface liquid, submucosal gland secretion and alveolar-capillary compartments. In July 2005, Dr. Song joined the Translational Research on Microbial Pathogens group at UCSF, and he is currently studying biomarkers and ventilator associated pneumonia (VAP), as well as pathophysiology of pseudomonas aeruginosa induced lung injury in a mouse model. One of Dr. Song’s aims is to find a biomarker that could be used to predict mortality and correlates with bacteria quantity and virulence in VAP patients.

Katherine Yang is an Assistant Clinical Professor in the Department of Clinical Pharmacy at the UCSF School of Pharmacy. Kathy received her doctorate in pharmacy (Pharm.D.) in 1998 and completed a Residency in Pharmacy Practice in 1999 and Residency in Infectious Diseases Pharmacotherapy in 2000. She then went on to obtain her MPH in Epidemiology from UC Berkeley in 2001. She has been a member of the faculty of the UCSF School of Pharmacy since 2001 and is also a member of the Clinical Infectious Diseases Consult Service at UCSF Medical Center. Her research focuses on programs and techniques to increase the appropriate use of antimicrobial agents in the intensive care setting. She is currently conducting a study to determine the effectiveness of a multi-disciplinary antimicrobial management program in preventing overuse of unnecessary antibiotics and development of antimicrobial resistance in the ICU. She is particularly interested in the use of new molecular diagnostic techniques to rapidly detect infection as a mechanism of curbing unnecessary antibiotic use.

Hanjing Zhuo received her Bachelor of Medicine from Shanghai Medical University, China. After working in Zhongshan Hospital, which is affiliated with Shanghai Medical University, for 3 years, she moved to California and obtained a Master of Public Health (MPH) in Epidemiology/Biostatistics from University of California, Berkeley. In October 2003, she joined the Translational Research on Microbial Pathogens group at UCSF and was appointed as the project director of two NIH sponsored human clinical studies, one a Phase II clinical trial of new therapy for clinical acute lung injury and the other a prospective cohort study to explore the mechanisms of P. aeruginosa induced lung injury. Her responsibilities include overseeing patient recruitment and data collection for these studies as well as providing statistical analyses of the data. Hanjing also works closely with other collaborating research groups in database consultation and epidemiological analyses.