Biology on the Edge Upcoming Seminars
2009 - 2010 Speaker Series
September 18, 2009, 4:00-5:00PM, 535-152 Classroom
Animesh Ray, PhD
Title: "Networks and hypertension: how rare diseases can illuminate understanding of a common disease"
September 25, 2009, 4:00-5:00PM, 535-152 Classroom
Craig Adams, PhD
Title: "Prion's --- The Science and the Diagnostic Challenge"
Abstract: Prion diseases have a little something for everyone ---- cannibalism in the dark and wet jungles of New Guinea --- infectious agents that can withstand incineration at temperatures up to 600C. I will review some of the science surrounding prion disease and present a review of the diagnostic efforts and need to detect prion disease. Finally, there will be an overview of the collaborative effort between Dr. Stan Prusiner and Beckman Coulter to develop a test for "mad cow" disease.
November 13, 2009, 4:00-5:00PM, 535-152 Classroom
Susan Kane, Professor, Division of Tumor Cell Biology, City of Hope, Duarte, CA
Title: "Laboratory Models of Drug Resistance in Cancer"
Abstract: The development of multidrug resistance remains one of the most serious impediments to effective, curative chemotherapy in cancer patients. Resistance develops from a cancer cell's natural adaptive response to anticancer drugs. By understanding these cellular responses, we hope to learn more about the mechanism of action of specific drugs and about why treatments fail. I will present recent data pertaining to two main projects in the lab: 1) perhaps the best characterized mechanism of drug resistance is that mediated by the Multidrug Resistance-1 (MDR1) gene in humans. MDR1 codes for P-glycoprotein (Pgp), a plasma membrane protein that acts as a drug pump to prevent intracellular drug accumulation. Pgp can transport and confer resistance to a variety of anticancer agents, whereas Pgp expression in normal tissues can affect drug pharmacokinetics, pharmacodynamics, and blood-brain distribution in patients. We have developed a novel mouse model in which we visualize mouse mdr1 expression in vivo using luminescence-based bioimaging. With this model we can measure mdr1 expression in live animals, in real time, and under the influence of various environmental and genetic influences. 2) A second project is focused on resistance to trastuzumab (Herceptin), a monoclonal antibody directed against the Her2 receptor that is frequently overexpressed in human breast cancer. Trastuzumab is used clinically for the treatment of Her2-positive breast cancers, but only about 30% of those cancers actually respond to trastuzumab monotherapy. We have isolated trastuzumab-resistant cells in the laboratory and found that they have sustained activation of the PI-3-kinase/Akt pathway of signal transduction in the presence of trastuzumab, which normally turns off this pathway in Her2-dependent cells. Recent results point to the protein kinase A (PKA) pathway as an important mediator of sustained PI3K/Akt signaling, and dysregulation of that pathway as a mechanism of trastuzumab resistance. Current studies are focused on clarifying the mechanism by which PKA signaling impacts PI3K/Akt signaling and trastuzumab resistance.
November 20, 2009, 4:00-5:00PM, 535-152 Classroom
Nancy Schoenbrunner, PhD, Acting Director, Chemistry & Innovation Technologies
Roche Molecular Systems, Pleasanton, CA
Title: "The Molecular Toolbox: Innovations in Chemistry, Enzymology and Assay Design for TaqMan® PCR"
Abstract: Roche Molecular Diagnostics, the world's leading molecular diagnostics company, develops and commercializes highly sensitive diagnostic and blood screening tests based on the company's Nobel prize winning PCR and now industry-standard real-time PCR technologies. This talk will provide a description of tools developed at Roche Molecular to enhance the specificity and sensitivity of real-time PCR assays. The approaches presented include various hot start methods and primer modifications to increase specificity, thermal cycling and nucleotide modifications of probes to address target variability as well as designer DNA polymerases for improved reverse transcriptase activity.
December 4, 2009, 4:00-5:00PM, 535-152 Classroom
Helge Zieler, PhD, Synthetic Genomics, Inc., La Jolla, CA
Title: Breeding, Transgenesis and Genomics: A 21st Century Perspective on Plant Improvement"
Abstract: TBA
2008 - 2009 Speaker Series
Roland Contreras, Guest Speaker
"N-glycan from man to yeast"
January 7, 2009, 1:00 - 2:00 PM
Building 535, Room 152/154
Abstract: Here we provide a protocol for engineering the N-glycosylation pathway of the yeast Pichia pastoris. The general strategy consists of the disruption of an endogenous glycosyltransferase gene (OCH1) and the stepwise introduction of heterologous glycosylation enzymes. Each engineering step results in the introduction of one glycosidase or glycosyltransferase activity into the Pichia endoplasmic reticulum or Golgi complex and consists of a number of stages: transformation with the appropriate GlycoSwitch vector, small-scale cultivation of a number of transformants, sugar analysis and heterologous protein expression analysis. If desired, the resulting clone can be further engineered by repeating the procedure with the next GlycoSwitch vector. Each engineering step takes B3 weeks. The conversion of any wild-type Pichia strain into a strain that modifies its glycoproteins with Gal2GlcNAc2Man3GlcNAc2 N-glycans requires the introduction of five GlycoSwitch vectors. Three examples of the full engineering procedure are provided to illustrate the results that can be expected.
James Cregg, Ph.D., Professor
"Production of Recombinant Proteins in the Yeast Pichia pastoris"
January 16, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: As systems for the production of recombinant proteins, yeasts combine the growth and genetic manipulation advantages of bacteria with the ability to perform important post-translational modifications such as proper folding, proteolytic processing, disulfide bridge formation and glycosylation. Relative to Saccharomyces cerevisiae, Pichia pastoris has two significant physiological advantages as a host for the production of recombinant proteins. The first is the promoter used to transcribe most foreign genes, which is derived from the P. pastoris alcohol oxidase I gene (AOX1). This promoter is efficiently transcribed in cells exposed to methanol as the sole carbon source but is highly repressed under most other growth conditions. The second advantage is that P. pastoris does not have a tendency to ferment as does S. cerevisiae. A product of fermentation is ethanol, which can rapidly build to toxic levels in high-density cultures. As a consequence of these and other advantages, P. pastoris expression strains are easy to scale up from shake-flask cultures to large-volume fermenter cultures growing at cell densities of greater than 100 grams/liter, dry cell weight. The P. pastoris system is particularly valued for its ability to secrete recombinant proteins. Since the organism secretes only low levels of native proteins, the recombinant protein is often the major protein species in the medium.
Equally important to the success of P. pastoris as an expression system is its ready availability from a commercial source (Invitrogen, Carlsbad, CA USA). As a result, strains, expression vectors and technical instructions can be purchased at a nominal cost by both academic and commercial labs. Since 1994, when kits and other expression components were first released, the number of publications describing the production of recombinant proteins in P. pastoris has increased substantially every year with a total of over 1,800 publications now in print. The large variety of recombinant proteins has helped provide guidance to the types of proteins that the organism can and cannot synthesize well. It has also provided a large and diverse community of users that are available to provide technical assistance, and, in many cases, generate new and improved tools and techniques for the P. pastoris expression community.
David Sadava, Pritzker Family Foundation Professor of Biology, Joint Science Department, Professor-at-large, KGI, Adjunct Professor, Department of Tumor Cell Biology, City of Hope Medical Center
"Tresting Lung Cancer from Lab Bench to Bedside"
January 28, 2009, 1:00 - 2:00 PM
Building 535, Room 152/154
Abstract: With over 200,000 new cases last year and over 160,000 deaths in the US alone, lung cancer is a major medical challenge. Chemotherapy is a mainstay of treatment. However, most patients develop multi-drug resistance. I am investigating new ways to overcome this resistance, and will report on three of them. They range from a conventional approach, using a widely prescribed antimalarial drug; to a strategy using RNAi to selectively block a resistance mechanism; to employing natural products previously used in traditional medicine. In all cases, my approach has used cellular and molecular tools.
Yao-Liang Tang, MD, PhD, Research Associate Professor
"Preconditioning of Cardiac Stem Cells"
February 6, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: The rapid depletion of endogenous cardiac progenitor cell pool by myocardial infarction (MI) and the inefficient engraftment of ex vivo expanded progenitor cells limit the potential use of cardiac cell therapy. Recent studies have identified CXC chemokine SDF-1α and its receptor CXCR4 as critical mediators in ischemia-induced recruitment of bone marrow (BM)-derived circulating stem/progenitor cells. However, in cardiac stem/progenitor cells, the expression of CXCR4 is normally very low. Here, we studied the effects of hypoxia on the CXCR4 expression in cardiosphere-derived stem cells (CSCs) and on the homing capability of these cells to ischemic tissue. We found that hypoxic treatment of CSC cells upregulated HIF-1a-dependent CXCR4 expression, which markedly enhanced their migratory capacity and recruitment to the ischemic myocardium. Importantly, systemic infusion of hypoxic-preconditioned CSC cells into mice with surgically-induced MI resulted in a significantly reduced infarct size and improved cardiac function. Thus, hypoxic-pretreatment of cardiac stem/progenitor cells prior to transplant may offer additional therapeutic benefit by enhancing homing and retention of the cells to ischemic hearts.
Matt Croughan, George B. and Joy Rathmann Professor, Director of the Amgen Bioprocessing Center
"Learning Curves and Evolution of Industrial Bioprocesses"
February 13, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Industrial bioprocesses, as well as many other phenomena, frequently show a biphasic trend of improved performance over time. A steep, rapid first phase is generally followed by a long, steady second phase. This second phase data often follows a simple exponential form, showing a constant doubling time or halving time over many years. Several examples of this evolution pattern will be presented. Mechanistic theories to explain this pattern will be presented, including one based upon learning curves and another based upon evolution of objectives. Learning by doing versus learning before doing, as discussed by G. Pisano in his book "The Development Factory", will be explained. As firms gain increased understanding of their industrial bioprocesses, there is an evolution in the optimum learning approach. Modeling and prediction become increasingly valuable as theories are tested, refined, and hopefully validated by commercial performance data. Results from case studies will be used to highlight key points and discuss the business world implications of learning before doing versus learning by doing in biotechnology.
Arend Hintze, Postdoctoral Fellow
"A neutral random modular network growth model"
February 20, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Research on network modularity involves looking at many different networks, thinking about the same question over and over again: "How modular is this?" And after some time I realized that I have no intuitive measure of how modular or non modular something can be. So I wanted to design an algorithm that produces networks with all kinds of different topologies. Playing around with this algorithm and its parameters created many different graphs, even "anti" modular structures. Which ultimately lead to the conclusion that our present methods used are insufficient or at least inaccurate. This talk is all about "anti"-modularity, degree distributions, and all kinds of different and strange networks.
Dr. Steve Sommer, Founder & Senior Researcher, Medomics, M.D., Cornell University Medical College, New York, NY
"Clinical Molecular Diagnosis in the Era of Massively Parallel Sequencing: PAP/MAP for Monitoring of Therapy or Recurrence in Breast Cancer"
February 27, 2009 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Mortality from breast cancer may be reduced substantially if personalized therapy is instituted. Whole exome capture followed by massively parallel sequencing will soon be available to enumerate all the cancer-specific protein and microRNA structural changes. With this information, therapy can be instituted to leverage the enumerated "weaknesses" of the cancer. Once therapy is instituted, monitoring of therapy or recurrence (MOTOR) can be performed by utilizing the cancer signature in circulating cells. As a model system to demonstrate the efficacy of MOTOR, we analyzed plasma to detect breast cancer mutation signatures of DNA fragments released from apoptotic or necrotic cancer cells and the DNA of circulating cancer epithelial cells. Initially, candidate cancer genes were sequenced in breast cancer tissue samples to identify in each patient a personalized cancer signature of somatic mutations. Subsequently, pyrophosphorolysis activated polymerization (PAP) (www.cityofhope.org/PAP), a method for detecting ultra-rare mutations, was used to detect the cancer-specific signature in DNA isolated from the plasma and circulating epithelial cells of patients with non-metastatic breast cancer. Our data demonstrate the rapid development of PAP assays that routinely detect even a single copy of the cancer-specific somatic mutations in circulation. The selectivity of PAP is extremely high, often ranging from at least 1 part per million to as high as 1 part per billion. Circulating levels of cancer signature mutations and their rates of increase are being measured at multiple intervals in a multi-year follow up. Our ultimate goal is to achieve effective monitoring of chemotherapy and to predict recurrence months to years earlier than currently possible.
Chris MacDonald, Visiting Professor
"Direct-to-Consumer Genetic Testing: Consumer Empowerment or High-Tech Fortune- Telling?"
March 6, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Direct-to-Consumer genetic testing based on Genome-Wide Association Studies (GWAS) is to date the closest point of intersection between the biotechnology industry and the world of the average consumer. Such tests pose unique ethical challenges: they are health-related, and technically sophisticated, but their information value is highly debatable. Most discussions of ethical issues related to DTC testing have been dominated by biomedical questions and vocabulary -- "clinical utility," "appropriate use," and so on. This presentation seeks out categories of products to serve as a suitable comparison class for these tests, and asks how switching from a bioethics framework to a business ethics framework helps answer the relevant ethical questions.
Weng Ki Cheng, Postdoctoral Fellow
"Target specificity of quinolones and cell-wall inhibitors within functional families of sunthetic lethal Staphylococcus aureus temperature-sensitive mutants"
March 20, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: The synthetic lethality of weak antibacterial compounds and weakly performing target proteins has been used recently as a tool to confirm mechanism of action information for two families of known drug compounds: cell wall inhibitors and DNA replication inhibitors. We have used a collection of temperature sensitive essential-gene mutant alleles exposed to low amounts of known drugs to explore the target specificity of chemical-genetic synthetic lethal interactions. Synthetic lethality was investigated in a collection of 13 temperature sensitive Staphylococcus aureus mutant strains of DNA replication genes. Inhibitors of DNA gyrase, show unexpected potency toward these DNA replication mutants while little effect was observed when these DNA gyrase inhibitors were subjected to cell wall mutant strains. Synthetic lethality was also investigated in a collection of 5 temperature sensitive Staphylococcus aureus mutant strains of cell wall genes. Inhibitors of cell wall genes, show unexpected potency toward these cell wall mutants while no effect was observed when these cell wall inhibitors were subjected to DNA replication mutant strains. These findings suggest that synthetic lethality can occur between certain targets within the same functional family. This expands the potential utility of chemical-genetic synthetic lethal studies from a tool to identify mechanisms of action into a tool to identify functional interactions between members of a functional pathway.
Gail Baura, Professor
Continuous Drowiness Monitoring"
April 10, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Patient monitoring refers to the continuous observation of repeating events of physiologic function to guide therapy or to monitor the effectiveness of interventions. Traditionally, these medical devices were only used in hospital operating rooms (ORs) and intensive care units (ICUs). Over the last two decades, patient monitors have moved to other hospital wards and patient clinics. These days, a patient monitor may even be implanted in an ambulatory patient. This migration from the OR and ICU has been enabled by system theory. In this talk, a new type of patient monitor will be discussed. The goals for this continuous drowsiness monitor are incorporation into intelligent vehicle systems and assessment of neurologic function.
Molly Schmid, Professor
"Managing Fail Early Fail Fast Decisions in New Product Development"
April 17, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: This project explores the management of new product development of pharmaceuticals for human health. This process is characterized as long, expensive and risky and one that poses unique challenges for effective management. A successful drug discovery and development program takes 12-15 years, costs well over $800M, and only a small fraction of projects succeed. The Pharmaceutical Research and Manufacturers of America estimate that of the 5000 compounds that are synthesized in the lead optimization process, only one will progress to drug registration. Thus, failures represent substantial costs in terms of both dollars and time, and are the subject of much concern in the industry.
Early and rapid attrition of projects, described by the "fail early, fail fast" (FEFF) axiom, often guides project management in both the drug discovery and drug development stages. The FEFF principle aims to rapidly terminate projects with a perceived limited potential for success. By the early termination of projects that won't succeed, resources can be reallocated to projects where the potential for success is perceived to be higher, thereby optimizing the number of new drugs launched onto the market.
While the FEFF axiom makes intuitive sense, its validity relies on "perfect information" in which the ultimate outcome for the new drug can be predicted. In reality, "perfect information" is seldom available during the drug discovery and development process and so managers are unable to make "perfect" decisions. Therefore, the practice of FEFF may result in a high number of Type I errors, in which a project with the potential for success is terminated prematurely based on information available at the time a decision is made.
This work begins to examine the practice and impact of FEFF decisions, and focuses on the drug discovery stage of the pharmaceutical R&D pipeline. This stage represents nearly 40 percent of the time spent in bringing a drug to market, and is understudied relative to the development stage. In this study, we introduce the notion of "innovation litter", which can be used to retrospectively study how the innovation process and FEFF have been practiced in different firms. Metrics are developed to measure FEFF behaviour, to identify projects that were and were not subject to FEFF decisions, and to uniquely characterize the shape of the drug discovery and development pipelines in large and small firms. By using these metrics, drug discovery managers may make better decisions about the allocation of R&D expenditure for optimal effectiveness. Since management practices undertaken during the drug discovery stage are fully under the control of an individual pharmaceutical company, rather than regulatory agencies, optimization of decision-making in this stage presents an enormous opportunity to create a competitive advantage to the innovating firm.
Greg Dewey, PhD, Finnigan Professor
"Three Research Vignettes"
April 24, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Three different research projects in my lab will be discussed. The first deals with a time series analysis of gene expression profiles in breast tumor cell lines. A linear response model is used to create a gene regulatory network that can be a data mining device for identifying cancer specific effects. The second deals with a topological algorithm to compare protein structures. This algorithm maps a local geometric measure onto an alphabet and then uses conventional sequence alignment methods to do structure alignment. The third topic is a short description of Bayesian networks and how they are used to infer causal relationships in cellular signaling.
Alpan Raval, Associate Professor
"Entropic Identification of Genomic Islands"
May 15, 2009, 4:00 - 5:00 PM
Building 535, Room 152/154
Abstract: Perhaps the most dramatic examples of inter-species gene transfer in bacteria are provided by genomic islands, regions of dozens or hundreds of genes introduced from unrelated organisms whose encoded products can provide complex, niche-defining functions. While the recognition of genomic islands can be a powerful mechanism foridentifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. Rather, identification of genomic islands usually begins with cataloguing individual genes likely to have been recently introduced into the genome. Regions with a high density of putative alien genes are then examined for other features suggestive of recent acquisition of a large genomic region. The weakness of these "bottom-up" approaches lies in the difficulty of identifying robustly those genes which are atypical due to recent foreign ancestry. An alternative "top-down" approach is presented where bacterial genomes are recursively divided into progressively smaller regions with distinct compositional signatures. Thus large chromosomal regions with atypical features are identified with high confidence due to the simultaneous analysis of multiple genes. This approach is based on a generalized entropic divergence measure to quantify compositional differences between genomic segments in a statistical framework. The proposed genome island prediction algorithm was tested on both artificial chimeric genomes and genuine bacterial genomes.
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