Opthalmologist on a chip: Fully integrated microfluidic tear osmolality and protein biomarker quantification for dry eye stratification

Kelly Karns

Ph.D. Candidate, Professor Amy Herr’s Lab, UC Berkeley

Abstract

Human tear film fluid offers tremendous potential as a non-invasive diagnostic fluid. However, the use of tear fluid in diagnostic medicine is limited owing to non-standardized collection methodologies and low volume availability. I will present a first-reported microfluidic tear fluid biomarker assay which will serve as a foundation for both rapid biomarker validation and point-of-care ocular diagnostics. Our microfluidic approach demonstrates multiplexed quantitation of both tear fluid osmolality and lactoferrin (Lf) protein concentration in microliter quantities of human tear fluid from healthy and Sjögren’s syndrome (SS) patients. Lf is a tear-specific biomarker for SS, a serious systemic autoimmune disease currently diagnosed through rudimentary tear volume, ocular surface chemistry measurements and an invasive lip biopsy. Meanwhile, tear osmolality is a putative marker of overall dry eye disease severity and can provide a quantitative assessment for patient-specific treatment. Taken in sum, this work details important steps toward (1) expanding the set of proteins quantified by electrophoretic immunoassays to encompass a wider range of isoelectric points than has been reported, (2) creating a first-in-kind translatable assay with clinical relevance to SS and dry eye diagnostics, and (3) expanding the analytical toolkit available for rapid biochemical measurements in tears, as is relevant to the advancement of basic research and clinical medicine.

Speaker Biography

Kelly Karns is a Ph.D. Candidate in Professor Amy Herr’s lab. She received a B.S. in Bioengineering and Mechanical Engineering from Yale in 2007 and an MS in Bioscience Enterprise in 2008 before joining the Joint Graduate Group in Bioengineering at UC Berkeley/UCSF. She is currently working to miniaturize traditional laboratory biochemical analysis techniques for applications requiring the use of small sample volumes.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, faculty, or other outside speakers affiliated with POCDx.

This video was originally recorded on October 25th, 2011 in 621 Stanley Hall, UC Berkeley

Navigating the Venture Capital Funding Process

Toby Prosky

Principal, Founders Fund

Are you interested in securing venture capital to get your medical device startup off the ground? Toby Prosky will bring his unique perspective as a VC at a premier fund focused on revolutionary innovations to the table. He will be covering topics including:

• Practical thoughts on the venture funding process: getting the attention from VCs that your idea deserves.
• What are venture capitalists looking for?
• When is the right time to look for venture funding?
• What are healthcare-specific pitfalls to avoid?
• Dos and don’ts when presenting your idea.

Speaker Biography

Toby Prosky is a principal at Founders Fund. In addition to reviewing deals and performing financial analysis on portfolio companies, Toby assists Founders Fund companies with operational matters. Toby joined Founders Fund from Maxim Group, a boutique investment bank, where he headed the firm’s West Coast capital markets efforts. Toby has also worked for American Express, Merrill Lynch, and Brean Murray, Carret & Co. Prior to his career in finance, Toby was on the faculty of University of North Carolina at Asheville, where he taught courses in ancient Greek literature and post-modern theory. Toby holds a BA in Philosophy from UNC – A and an MA in Philosophy from the Katholieke Universiteit Leuven (Belgium).

About Founders Fund (via CrunchBase):
Founders Fund is a San Francisco based venture capital firm which invests at every stage in companies with revolutionary technologies. The firm’s six partners, Peter Thiel, Sean Parker, Ken Howery, Luke Nosek, Bruce Gibney, and Brian Singerman have been founders of or early investors in numerous well-known companies such as Facebook, PayPal, Napster, and Palantir Technologies. Founders Fund was formed in 2005 and has launched three funds to date with more than $500 million in aggregate capital under management..

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, faculty, or other outside speakers affiliated with POCDx.

This video was originally recorded on October 11th, 2011 in 621 Stanley Hall, UC Berkeley

The POCDx Idea Lab will be holding its annual kickoff meeting on Tuesday, September 13th at 6pm in 621 Stanley Hall. Rick will be giving a brief overview of the Enabling Point of Care Diagnostics Conference he recently spoke at, with officer elections being held shortly thereafter.  Food and drinks will be served and a good time will be had by all!

The Role of Diagnostics in Infectious Disease Control: A Look at TB in the San Francisco Area

Dr. Masae Kawamura

Director, Tuberculosis Control Program, San Francisco Department of Public Health

Abstract

Dr. Kawamura will present the challenges associated with tuberculosis control in the San Francisco area, as well as some of their ongoing and investigational initiatives to combat the spread of the disease through innovative diagnostic tools.

Speaker Biography

Masae Kawamura, MD has been a tuberculosis (TB) clinician for more than 20 years, serving as Director of San Francisco’s TB Control Program since 1996. Under her leadership, San Francisco became the first jurisdiction in the U.S. to implement Interferon gamma release assay (IGRA) blood testing for TB. Currently, TB Control is also participating in studies preliminary to acceptance of the new sputum-sample based GeneXpert TB test, from Cepheid.

A Co-Principal Investigator for Curry National TB Center, a CDC–affiliated Regional Training and Medical Consultation Center, Dr. Kawamura has served on the faculty since its inception in 1994. She also served on the CDC Advisory Council for the Elimination of TB (ACET) for eight years, the last three as chair, and continues to serve on subcommittees of the group. Dr. Kawamura is an assistant clinical professor at the University of California–San Francisco (UCSF) and has coauthored numerous TB publications. She is currently president of the International Union Against Tuberculosis and Lung Disease (IUATLD), North American Region.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, faculty, or other outside speakers affiliated with POCDx.

This video was originally recorded on May 24th, 2011 in 621 Stanley Hall, UC Berkeley

Microchip-based point-of-care (POC) technologies to measure HIV-1 viral load information

Utkan Demerci, Ph.D.

Assistant Professor of Medicine and Health Sciences and Technology, Harvard University Medical School and MIT

Abstract

Currently, more than 30 million people are living with HIV-1 worldwide. Based on 2010 WHO guidelines (treatment initiation at CD4 cell count <350 cells/mm3), only approximately 36% AIDS patients are receiving anti-retroviral therapy (ART) in low- and middle-income countries. The low coverage of ART program is mainly due to the lack of cost-effective diagnostics to monitor CD4 cell count and viral load in AIDS patients in resource-limited settings, despite the fact that first-line ARV drugs become cheaper or even free. To overcome this challenge, we developed microchip-based point-of-care (POC) technologies to count CD4+ T lymphocytes and provide viral load information. On a microchip coated with immobilized antibodies, CD4 T lymphocytes were captured from whole blood and subsequently counted using a lensless image technology. This portable, battery operated, lensless, microchip platform showed significant correlation in CD4 T-cell counts compared with the gold standard, i.e., FACS counts both at BWH in Boston (r: 0.94, p<0.01), and MUHAS in Tanzania (r: 0.49, p<0.01). The device rapidly produced CD4 T-cell counts within 10 minutes using an automated cell counting program. Using a similar microchip platform, HIV was also be captured by immobilized antibody and detected by quantum dot based staining. In conclusion, this microchip platform technology can potentially deliver inexpensive, rapid and simple testing to monitor antiretroviral treatment in resource-limited settings.

Speaker Biography

Utkan Demirci, Ph.D., is an Assistant Professor of Medicine and Health Sciences and Technology at Harvard University Medical School and MIT (Massachusetts Institute of Technology). Dr. Demirci received his B.S. degree in Electrical Engineering in 1999 as a James B. Angell Scholar (Summa Cum Laude) from University of Michigan, Ann Arbor. He received his M.S. degree in 2001 in Electrical Engineering, M.S. degree in Management Science and Engineering in 2005 and Ph.D. in Electrical Engineering in 2005 all from Stanford University. In 2008, Dr Demirci was given Department of Medicine, Harvard Medical School-Young Investigator Award; The Outstanding Young Persons of the World, Junior Chamber International (JCI). In 2006, he was selected to TR-35 as one of the world’s top 35 young innovators under the age of 35 by the MIT Technology Review. Dr. Demirci has published more than 50 peer reviewed journal publications, more than 50 conference proceedings and 10 book chapters. His research interests involve applications of microelectromechanical systems (MEMS) and acoustics in medicine, especially: microfluidics for inexpensive CD4 counts for HIV in resource-limited-settings for global health problems; cell-by-cell 3D tissue printing; high-throughput blood biopreservation; oocyte vitrification. Dr. Demirci leads a group of 30 researchers focusing on nano and Sciences and Technology, Center for Bioengineering, Brigham and Women’s Hospital, Harvard Medical School.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, faculty, or other outside speakers affiliated with POCDx.

This video was originally recorded on April 25th, 2011 in 621 Stanley Hall, UC Berkeley

A meta-analysis of symptomatic visceral leishmaniasis diagnosis by in-house polymerase chain reaction assays

Danica Helb

Graduate Student Researcher, Rosenthal Lab, UC Berkeley

Abstract

Leishmaniasis is the third most important vector-borne disease worldwide. Identification of Leishmania amastigotes in bone marrow, spleen, or lymph node aspirates has conventionally been used to diagnose visceral disease. However, these methods are relatively insensitive and time consuming. In-house polymerase chain reaction tests are being developed to rapidly diagnose visceral leishmaniasis (VL) infections with high sensitivity and specificity. Meta-analytical methods were used to determine assay design parameters that were associated with higher estimates of diagnostic accuracy of in-house PCR assays to detect VL. PUBMED and EMBASE databases were searched for articles employing PCR to diagnose VL. Only studies that compared results of in-house PCR to a gold standard (microscopy or culture) were included. Sensitivity and specificity were used as measures of diagnostic accuracy, the outcome of interest, in a bivariate/hierarchical summary receiver operating characteristic model. After stratification by study design, clinical follow-up, PCR sample type, sample storage method, amplification and detection methods, and target gene, the data were re-analyzed. PCR-based diagnosis of VL appeared to be a promising alternative to microscopy, culture, and serology. Higher estimates of diagnostic accuracy were achieved when samples were stored in tubes than when samples were stored on filter paper prior to DNA extraction. Conventional PCR methods can be employed, reducing the costs associated with newer PCR techniques. Whole blood-based PCR detection of VL was highly sensitive and specific, and has the potential to eliminate the need for bone marrow samples and the invasive procedures associated with its collection.

Speaker Biography

Danica received her undergraduate degree in Biology from Bates College in Maine in 2002. Working in the Alland Lab at the University of Medicine & Dentistry of New Jersey after graduation, she was responsible for the research, development, and initial testing of the GeneXpert MTB/RIF. Developed in collaboration with Cepheid and the Foundation for Innovative New Diagnostics, the Xpert MTB/RIF assay, which integrates sputum processing, diagnosis of tuberculosis, and detection of drug resistance into a hands-free test, has recently been approved for use by the World Health Organization. Danica also worked as a consultant for FIND, performing testing and feasibility studies of Eiken’s TB-LAMP assay for diagnosis of tuberculosis in Vietnam. Danica received an MPH in Epidemiology in 2010, and is now a PhD student in Infectious Diseases & Immunity at UC Berkeley. She is currently investigating a potential new antimalarial drug target in the Rosenthal Lab at UC San Francisco.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, followed by discussion.  Students may choose to present their work or a recent journal article.

This video was originally recorded on March 8th, 2011 in 621 Stanley Hall, UC Berkeley

Developing on-demand, fully-integrated molecular diagnostic systems

Peter J. Dailey

Senior Vice President of Research & Development, Cepheid

Abstract

Cepheid based in Sunnyvale, Calif., is an on-demand molecular diagnostics company that develops, manufactures, and markets fully-integrated systems and tests for genetic analysis in the clinical, industrial and biothreat markets. The Company’s systems enable rapid, sophisticated genetic testing for organisms and genetic-based diseases by automating otherwise complex manual laboratory procedures. Cepheid’s easy-to-use systems integrate a number of complicated and time-intensive steps, including sample preparation, DNA amplification and detection, which enable the analysis of complex biological samples in its proprietary test cartridges. Through its strong molecular biology capabilities, the Company is focusing on those applications where rapid molecular testing is particularly important, such as identifying infectious disease and cancer in the clinical market. Cepheid currently markets IVD tests for use in the areas of Healthcare Acquired Infections (HAI), Critical Infectious Disease, and Women’s Health. The growing menu includes Xpert® SA Nasal Complete, Xpert® vanA, Xpert® C. difficile, Xpert® MRSA/SA SSTI, Xpert® MRSA/SA BC, Xpert® MRSA, Xpert® GBS, Xpert® EV, and Xpert® HemosIL® FII & FV.

Speaker Biography

Dr. Jennifer Glass is currently Director, Engineering at Cepheid and manages the Optical Engineering, System Integration, and Consumables groups. Prior to joining Cepheid she worked as a Sr. Device Engineer at Gemfire, an optical device company, specializing in polymer waveguides and 980nm pump sources for telecommunications. She received her Ph.D. in Physics from UC Berkeley in 2000, working with Professor Daniel Chemla at LBNL in the field of single fluorescent molecule detection, and she received her ’93 BA in Physics from Wellesley College where she focused her independent research in the field of Raman Spectroscopy.
Dr. Peter J. Dailey is Senior Vice President, Research and Development . Prior to joining Cepheid, Dr. Dailey was the Senior Director of the Department of Infectious Disease in Discovery Research at Roche Molecular Systems, Inc., from 2002 to 2006. He is a microbiologist and virologist by training and has worked in the field of diagnostic microbiology for the last 25 years. Dr. Dailey worked as a Public Health Microbiologist at the California State Dept. of Health’s Viral & Rickettsial Disease Laboratory in Berkeley, California in the 1980s on the development of diagnostic assays for HIV and HTLV. He also worked many years as a Clinical Laboratory microbiologist in medical centers, hospitals, and reference laboratories. Beginning in 1990, he was employed at Chiron Diagnostics (now Bayer Diagnostics) working on the research, development, and application of nucleic acid probe assays, in particular viral load assays for HCV, HIV, and SIV. He has served as a subcommittee member on the National Committee for Clinical Laboratory Standards committee revising Guidelines for Molecular Diagnostic Methods for Infectious Diseases and has authored or co-authored more than 35 peer-reviewed papers as well as several book chapters and reviews on infectious disease nucleic acid diagnostic assays.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, followed by discussion.  Students may choose to present their work or a recent journal article.

This video was originally recorded on February 22nd, 2011 in 621 Stanley Hall, UC Berkeley

Advanced sample preparation measures towards integrated molecular diagnostic devices for blood sepsis

Debkishore Mitra

Graduate Student Researcher, Luke Lee Lab, UC Berkeley

Abstract

Sepsis is a condition in which the human body is fighting a severe microbial infection that has spread through the blood stream. Early diagnosis of sepsis would increase the effectiveness of the present antibiotic therapies through rapid treatment, and could also be used for detecting contamination in blood bags before transfusion. However, the main diagnostic techniques currently available take days for diagnosis (e.g. blood cultures), lack portability and are expensive (e.g. RT-PCR based techniques). We propose here a portable, robust and microfluidic integrated molecular diagnostic system (iMDs) for blood sepsis diagnosis. This device would detect the presence of microbial contaminants in blood by employing an isothermal nucleic acid amplification technique known as Recombinase Polymerase Amplification (RPA) with fluorescent readout. This technique works at 37°C, reducing the energy and time needs for heating and cooling cycles, as in conventional PCR, and has simple microfluidic implementation. The device includes an upstream sample preparation module that separates bacterial and human DNA, improving specificity of detection. This module leverages the difference in membrane properties between human and bacterial cells to selectively lyse human cells in the device. This device, which can detect bacteria in microliters of blood, will be important for the detection, prevention, and treatment of blood sepsis as well as other bacterial diseases.

Speaker Biography

Debkishore got his undergraduate degree in Biotechnology from the Indian Institute of Technology, Kharagpur, India in 2008. During his undergraduate tenure he worked on a variety of projects, ranging from cell and molecular biology to bioinformatics. His undergraduate thesis work was done under Prof. A.K. Das in the Structural Biology Lab on the in-silico design of drugs against tuberculosis. Debkishore is currently a graduate student in the Joint Graduate Group in Bioengineering at UCSF/Berkeley, and is presently working on the development of diagnostic devices using microfluidics and MEMS technology.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, followed by discussion.  Students may choose to present their work or a recent journal article.

This video was originally recorded on February 8th, 2011 in 621 Stanley Hall, UC Berkeley

Funding point of care diagnostic technologies – how BVGH is bridging the gap

Elizabeth Ponder

Manager of Scientific Affairs, BIO Ventures for Global Health

Abstract

At BIO Ventures for Global Health (BVGH), our goal is to help for-profit companies find ways to participate in global health. We believe it is essential to engage private-sector innovators—particularly entrepreneurial biotechnology companies with a track record of developing new products—in the effort to prevent, diagnose, and treat neglected diseases in the developing world. Point of care diagnostics (POC Dx) represent an area of innovation that has the potential to significantly improve the quality of healthcare provided in resource poor settings of the developing world. However, a lack of financial incentives prevents for-profit organizations, especially key biotech innovators, from working in this area. BVGH is currently developing a milestone-based financial incentive as a novel funding mechanism to encourage participation in POC Dx development. Using the example of a panel for differential diagnosis of fever, we can highlight how this type of funding mechanism can help bridge innovation gaps and address a significant global health need.

Speaker Biography

Elizabeth Ponder joined BIO Ventures for Global Health (BVGH) in August 2010 as the Manager of Scientific Affairs. Dr. Ponder has a broad background and interest in infectious diseases and extensive experience in the field of parasitology. Her previous scientific research as a graduate student and postdoctoral fellow focused on using small molecules to explore the biological function and drug target potential of proteases of the parasite that causes human malaria. Prior to joining BVGH, Dr. Ponder worked as a Malaria Control Intern with The MENTOR Initiative in northeastern Kenya on a program to improve malaria diagnosis, treatment, and prevention in rural communities.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, followed by discussion.  Students may choose to present their work or a recent journal article.

This video was originally recorded on January 25th, 2011 in 621 Stanley Hall, UC Berkeley

Viruses in Haystacks: Detection and discovery of viral pathogens in acute pediatric illness in Nicaragua

Nathan Yozwiak

Graduate Student Researcher, Eva Harris (UCB) and Joseph DeRisi (UCSF) labs

Abstract

Monitoring the international emergence and spread of human pathogens is critical to global public health efforts aimed at preventing and treating infectious disease. Viral surveillance studies yield important information about the prevalence and seasonality of circulating virus species and the possible existence of novel species, yet many large diagnostic studies that have been conducted in temperate countries have not been repeated in tropical settings. Viral burden and incidence variations are likely to exist between such settings because of inherent environmental and social differences. The purpose of this study is twofold: to use the best available diagnostic technologies, including viral microarrays and deep sequencing, to delineate the spectrum of viral pathogens in a developing tropical environment with respect to acute respiratory illnesses and dengue-like illnesses and to utilize the data provided by the extensive screening as a platform for the discovery of novel or divergent human viral pathogens. In this study, we report the identification and complete genome sequence of a novel enterovirus isolated from a case of acute respiratory illness in a Nicaraguan child. Unbiased deep sequencing of nucleic acids from a nose and throat swab sample enabled rapid recovery of the full-genome sequence.

Speaker Biography

Nathan got his B.S. in Molecular and Cellular Biology from Johns Hopkins University in 2005. He is a PhD Candidate in Infectious Disease and Immunity at UC Berkeley under Eva Harris (UCB) and Joseph DeRisi (UCSF) and is expecting to graduate in May 2011.

About the Point-of-Care Diagnostics Idea Lab

The Point-of-Care Diagnostics (POCDx) Idea Lab was created as a forum for graduate students who are working in the areas of medical diagnostics and global health to discuss topics relevant to their research.  Students working in the areas of engineering, science, policy, and healthcare are encouraged to attend.  The bi-weekly meetings will be informal and will usually include one or two short presentations by graduate students, followed by discussion.  Students may choose to present their work or a recent journal article.

This video was originally recorded on November 2nd, 2010 in 621 Stanley Hall, UC Berkeley