2010 Nanobiotechnology Seminar Series

Seminar & Discussion 4:30 - 5:30 pm
Reception 5:30 - 6:00 pm

January 19, 2010 Munzer Auditorium

Edward H. Egelman, PhD 
Dept. of Biochemistry and Molecular Genetics
University of Virginia

Polymers and Pathogenesis: New Structural Insights 

Protein polymers are ubiquitous in biology, from cytoskeletal filaments to bacterial pili, and in many cases contain most of the protein in the cell. While it has been assumed that each polymer has a defined structure, we can show using electron cryo-microscopy and computational image analysis that many polymers exist in a multiplicity of states. Conserved subunits, such as bacterial flagellin or Type IV pilin, can be assembled in different ways, giving rise to abrupt changes in quaternary structure. As new quaternary structures emerge, these can have very new functions. For example, the bacterial ParM protein, a homolog of eukaryotic actin, forms filaments that are very different in structure than F-actin, and have very different functions. These insights suggest an under-appreciated mechanism for evolutionary divergence.

 Feb 16, 2010 Munzer Auditorium

Rashid Bashir, PhD 
Bliss Professor
Dept. of Electrical and Computer Engineering & Bioengineering
University of Illinois

Interfacing Biology and Silicon at the Micro and Nanoscale: Opportunities and Prospects 

Nanotechnology and BioMEMS can have a significant impact on medicine and biology in the areas of single cell detection, diagnosis and combating disease, providing specificity of drug delivery for therapy, and avoiding time consuming steps to provide faster results and solutions to the patient. Integration of biology and fabrication methods at the micro and nano scale offers tremendous opportunities for solving important problems in biology and medicine and to enable a wide range of applications in diagnostics, therapeutics, and tissue engineering. In this talk, we will present an overview of our work in Silicon-Based BioMEMS and Bionanotechnology and discuss the state of the art and the future challenges and opportunities. We will review a range of projects in our group focused towards developing rapid detection of biological entities and developing point of care devices using electrical or mechanical phenomenon at the micro and nano scale. We will present our work on developing silicon-based Petri dishes-on-a-chip, silicon based nano-pores for detection of DNA, silicon field-effect sensors for detection of DNA and proteins, and use of mechanical sensors for characterization of living cells.

Mar 2, 2010 CISX 101 Auditorium

Mauro Ferrari, Ph.D. 
University Endowed Chair in Biomedical Engineering
Professor and Chairman
Department of Nanomedicine and Biomedical Engineering (nBME)
Professor of Internal Medicine
The University of Texas Health Science Center - Houston
Webcast Talk Not Available Designer Nanotherapeutics - A Prelude and Fugue 

Therapeutics by design are the heart of individualized cancer medicine. Individualization, in turn, comprises no less than four dimensions: Spatial specificity of delivery of therapeutic action, temporal specificity of release of therapeutic agents, rapid monitoring of therapeutic and adverse effects, and engagement with the host biology. All four of these are enabled by recent progresses of nanotechnology - and hopefully will be even more in the future. All four of these have a profound link to the dynamics of mass transport at the nanoscale - and actually provide a prism for viewing cancer in a different light, which is quite mechanical in nature. (The key is E Minor). 

Apr 6, 2010 CISX 101 Auditorium

Alexander Wei, Ph.D. 
Professor of Chemistry and University Faculty Scholar
Dept. of Chemistry
Purdue University

Targeted Delivery of Gold Nanorods and Other Plasmonic Nanostructures: en route to Theragnosis 

Gold nanorods and nanostars can couple with electromagnetic irradiation at visible and near-infrared frequencies, and serve as multifunctional agents in biophotonic applications. These anisotropic nanostructures are capable of both linear and nonlinear optical responses, due in large part to polarization-sensitive modes that can be tuned by various structural and materials factors. Both types of particles have been used in biological imaging, but diverge with respect to their specific application. Gold nanorods are particularly efficient at converting optical energy into heat, and have been used to deliver intense photothermal effects with subcellular precision, guided by two-photon excited luminescence. Gold nanostars can be synthesized with magnetic cores to support a dynamic (gyromagnetic) mode of NIR imaging, effective at enhancing contrast in heterogeneous media such as those encountered in tissues. Recent advances will be presented in the context of their impact on theranostics and nanomedicine. 

Apr 20, 2010 CISX 101 Auditorium

Andreas Hoenger, Ph.D. 
Associate Professor
Dept. of Molecular, Cellular and Developmental Biology
University of Colorado at Boulder

A multi-scale approach to cell structure and function 

Technical Aspects: Microtubules are highly dynamic cytoskeletal structures that are involved in various cellular functions, by interacting with a diverse group of proteins. These proteins or protein complexes are typically grouped into molecular motors (kinesins, dyneins) and non-motor MAPs (Tau, TPX, EB1 etc.). Many of these proteins, including the dimeric microtubule building block αβ-tubulin itself have been extensively studied in vitro and their structure has been solved to near atomic detail. Many kinesin motor head domains and some MAPs have been analyzed in complex with microtubules by 3-D cryo-electron microscopy (cryo-EM). Most of the cryo-EM studies were performed in vitro and with so- called 3-D averaging procedures such as helical reconstruction, assuming a particular (e.g. helical) symmetry in the complexes. However, the recent rise of cryo-electron tomography (cryo-ET), promoted by new microscopy hardware such as large sensitive detectors, but also by new developments in tomographic reconstruction software opened new avenues for 3-D studies on large intracellular organelles and macromolecular assemblies. Also, cryo-sectioning performed on vitrified samples without the need for substitution and embedding prior to sectioning is an emerging technology that opens completely new possibilities in observing cellular structures at native conditions. Here an outlook is presented into the possibilities as well as the current limitations of cryo-ET and vitrified sectioning for high-resolution structural analysis in cell biology. New in vitro and in situ labeling methods are now being developed to mark protein complexes by high-density labels such as little metal clusters, which are either large enough for direct visualization, or to be detected by difference mapping. The parallel assignment of multiple labels may be achieved by electron energy-loss spectroscopy. This will allow for multiple labeling for EM that compares to different colors commonly used in fluorescence microcopy.

Biological in situ Example: One of the most challenging aspects when leaving the simple environment of an in vitro approach and venturing into the complex environment of an intact cell is the assignment of density boundaries between complexes as well as the unambiguous identification of structural elements within a complex. To this end we present our 3-D study on the ventral disk of Giardia. Giardia intestinalis is a unicellular, flagellated parasite of mammals, infecting ~1 billion people worldwide. Giardiasis is caused by ingesting water contaminated with cysts, which then excyst into trophozoites in the duodenum of the host. The trophozoite has a highly specialized microtubule (MT) cytoskeleton—4 pairs of structurally distinct flagella, and the ventral disc (VD). Trophozoites attach and detach from intestinal epithelia by a coordinated action of the cytoskeleton within the VD. Our large-area tomography data shows the VD consists of an array of ~45 parallel MTs that forms a counter-clockwise spiral ~8.5μm in diameter. Each VD MT has a micro-ribbon (MR) that extends ~200nm from the dorsal side of the MT into the cytoplasm and occurs along the entire length of the MT (3-7um). MRs connect laterally to each other via bridging elements. We have isolated the cytoskeletons of trophozoites and prepared them for cryo-electron tomography. We used our volume-averaging program, PEET, to average segments of 16nm long axial repeats (2 αβ-tubulin dimers) along VD MTs. Averages were calculated either from individual tomograms, or included all 6 tomograms (7400 repeats). A large protein complex, called the side-arm is found every 8nm (1 αβ-tubulin dimer) along the length of VD MTs. The side-arms span 5 protofilaments and have various linkers among them and to their neighboring side- arms, such that all are connected together along the length of the MT. The MRs are made of 3 parallel sheets with repeating structures along their length. There is a linker-bridge between the MR and a protofilament of the MT every 16nm. Individual tomograms have averages that are distinct from each other, with the greatest variety occurring in the side-arms. Our data suggests that an estimated 25,000 side-arms are working in concert with each other and the MRs to induce coordinated conformational changes within the VD driving attachment and detachment.

May 18, 2010 Clark Auditorium


Bruce Cohen, Ph.D.
LBNL Staff Scientist
Materials Sciences Division, The Molecular Foundry
Biological Nanostructures Laboratory
Lawrence Berkeley National Laboratory (LBNL)

Smart Nanoparticles for Cellular Imaging 

Certain nanoparticles possess unusual optical properties that may be of great value in imaging and microscopy. We have recently developed photoactivatable nanoparticles - called caged quantum dots - that are non-luminescent under typical microscopic illumination but can be activated with stronger pulses of UV light. These nanoparticles’ unique optical properties arise from the interaction between a classic organic caging group and a semiconducting quantum dot (QD), and while caging is dependent on the emission of the QD, it is effective through the visible spectrum into the nIR, offering a large array of new colors for photoactivatable probes. We have demonstrated that these QDs can be photoactivated within live cells and have examined the physical basis of the interaction between caging group and QD. For single molecule studies, we have found that a second type of nanoparticle - a lanthanide-doped upconverting nanoparticle (UCNP, below) - shows nearly ideal optical properties. UCNPs absorb two photons in the nIR and emit one at shorter wavelengths in the visible or nIR. UCNPs emit "anti-Stokes" light, producing a higher-energy photon from multiple lower-energy photos, and because nothing in the cell measurably emits anti-Stokes, there is minimal or no background autoflourescence. We have recorded the first single molecule images of UCNPs and find that they do not blink (as QDs ad many organic probes do) and that they posses remarkable photostability, resisting photobleaching under continuous irradiation long after organic dyes, proteins, and even QDs are extinguished. Through combinatorial methods, we have recently developed control over the both excitation and emission wavelengths of UCNPs, making multicolor upconverted imaging possible.

June 22, 2010 Munzer Auditorium

Mansoor Amiji, Ph.D. 
Professor of Pharmaceutical Sciences
Associate Chairman, Department of Pharmaceutical Sciences
Co-Director, Nanomedicine Education and Research Consortium (NERC)
Northeastern University

Multifunctional Nanosystems for Early Diagnosis & Targeted Therapy 

There has been tremendous recent interest in nanotechnology application for disease prevention, diagnosis, and treatment. For many diseases, such as cancer, early diagnosis and overcoming biological barriers and target specific delivery are the key challenges. Additionally, newer generation of molecular therapies, such as gene therapy oligonucleotides, and RNA interference, require robust and highly specific intracellular delivery strategies for effective therapeutic outcomes.

In this presentation, I will provide an overview of our work over few years in nanotechnology for target specific delivery of drugs and genes. We have developed metal, polymer, and lipid-based nano-platforms for diagnosis and delivery of therapeutics and image contrast agents. Peptide-modified gold nanostructures were developed for early cancer detection. Using biodegradable polymers, we have formulated nanocarriers for systemic delivery of hydrophobic anticancer drugs and therapeutic genes. Additionally, we have developed nanoemulsions, using oils rich in omega-3 polyunsaturated fatty acids, which can facilitate drug delivery across different biological barriers, such as the blood-brain barrier.

July 20, 2010 Munzer Auditorium

Robert Blumenthal, Ph.D. 
Program Director
Center for Cancer Reseach Nanobiology Program
National Cancer Institute

Nanochemistry in Membranes: Applications to Vaccines and Chemotherapy 

We are developing a new chemical nanobiology that involves reaction of photo-activable probes within a membrane, which serves as a 50 nm, highly organized hydrophobic container. We have used the membrane bilayer specific probe iodonaphthylazide (INA) that reacts with proteins and lipids following activation in situ either by direct UV irradiation or by energy transfer from a variety of donor chromophores. We have used this method in an analytic model to establish which proteins of the viral envelope penetrate the target cell membrane in the course of infection. The covalent modification of membrane proteins and lipids also modifies the function of membrane proteins. When applied to enveloped viruses, the treatment resulted in a complete loss of infectivity due to a loss of function of viral fusion proteins. We have shown the wide applicability of this inactivation technique to HIV, Influenza, Ebola, Marburg, Dengue and VEE viruses. By exclusively targeting the lipidic domain, exposed epitopes are preserved making the inactivated pathogens excellent vaccine candidates potentially applicable to cancer vaccines. When applied to whole cells the treatment resulted in loss of signaling function of cell surface receptors and loss of transport function of multi drug resistance transporters. Overall, photo-activation of INA in various cell lines, including those over-expressing the multi-drug resistance transporters leads to apoptosis. We are developing this new modality for cancer treatment using small hydrophobic molecules that can be turned into tumor killing toxic compounds by targeted radiation and ultrasound. I will also discuss ways in which light or heat can trigger physical-chemical changes in liposomal membranes resulting in localized release of drugs.

Aug 17, 2010 Munzer Auditorium

Joe W. Gray, Ph.D.
Staff Scientist/Direcor
Life Sciences Division
Dept. of Cancer and DNA Damage Responses
Lawrence Berkeley National Laboratory

An Omic View of Signaling in Cancer 

Modern omic measurements demonstrate the existence of a growing number of recurrent molecular subtypes in breast cancer. Assessment of responses to signaling pathway targeted therapeutic compounds in a panel of 60 breast cancer cell lines reveals differences in signaling behavior between cancer subtypes that should be taken into account during clinical deployment of new and approved therapeutic compounds. Assessment of responses to pathway targeted compounds in cells grown in different microenviroments suggests the need to assess response in histological context. Approaches to assessment of pathway activity in situ that are now under development will be discussed. 

Sept 21, 2010 CISX 101 Auditorium

Wah Chiu, Ph.D. 
Alvin Romansky Professor
Depts. of Biochemistry and Molecular Biology, Molecular and Cellular Biology, Molecular Physiciology and Biophysics, Molecular Virology and Microbiology Baylor College of Medicine

Visual Biology of Molecular Machines and Cells 

Single particle cryo-EM is now capable of resolving structures of molecular machines such as chaperonins and viruses better than 4.5 Å resolution. In the best scenario, one can trace protein backbone and visualize side-chains in a cryo-EM density map determined at this resolution. Advantages of cryo-EM imaging technique are to determine structure without invoking crystallography and to keep the specimen at a chosen solution state or in a cell-like environment. In addition, cryo-EM is also capable to resolve molecular details of protein aggregates and cells. Examples will be presented to demonstrate the types of structure information useful for understanding the functional mechanisms of molecular machines, protein aggregates and cells.

Oct 19, 2010 CISX 101 Auditorium

Michael Heller, Ph.D. 
Dept. of Nanoengineering, Dept. of Bioengineering & UCSD Moores Cancer Center
Univ. of California, San Diego

Detection of Cancer Related DNA Nanoparticle Biomarkers and Nanoparticles in Whole Blood 

While the potential medical applications of nanotechnology are rapidly growing, a number of issues still need to be resolved before nanomedicine moves from the lab to the bedside. Two very important challenges in nanomedicine will be the detection of early disease nanoparticulate biomarkers, and the monitoring of drug delivery nanoparticles. The ability to rapidly detect low levels of cell free circulating (cfc) DNA, RNA and other nanoparticulate biomarkers directly in blood would represent a major advance for early cancer detection and screening, residual disease detection and chemotherapy monitoring. Unfortunately, the process for isolating these nanoparticulate biomarkers from whole blood is complex, expensive and time consuming. Additionally, with the enormous amount of activity now being directed at new drug delivery nanoparticle therapeutics, it will also be important to develop rapid, sensitive and inexpensive monitoring techniques for this nanomedicine application.Thus, there is a critical need for novel robust technology, which will allow a variety of important nanoscale entities to be manipulated, isolated and rapidly detected directly from whole blood and other biological samples. Recently, we have developed a high conductance dielectrophoretic (HC-DEP) method that allows both hmw-DNA nanoparticulates and nanoparticles to be isolated and detected under high ionic strength conditions (Krishnan R., Sullivan B.D., Mifflin R.L., Esener S.C., & Heller M.J., Alternating current electrokinetic separation and detection of DNA nanoparticles in high-conductance solutions. Electrophoresis 29, 1765-1774, 2008; Krishnan R. & Heller M.J., An AC electrokinetic method for enhanced detection of DNA nanoparticles. J. Biophotonics 2, 253-2612009; Krishnan R., Dehlinger D.A., Gemmen G.J., Mifflin R.L., Esener S.C., & Heller M.J., Interaction of nanoparticles at the DEP microelectrode interface under high conductance conditions, Electrochem. Comm. 11, 1661-1666, 2009). We now show that a microarray DEP device can be used to rapidly isolate and detect high molecular weight (hmw) DNA nanoparticulates and nanoparticles directly from whole blood. At DEP frequencies of 5kHz-10kHz both fluorescent-stained hmw-DNA and 40nm fluorescent nanoparticles separate from the blood and become highly concentrated at specific DEP high field regions over the microelectrodes, while blood cells move to the DEP low field regions. The blood cells can then be removed by a simple fluidic wash while the hmw-DNA and nanoparticles remain highly concentrated. The hmw-DNA could be detected at a level of <260ng/ml, and the nanoparticles at <9.5 x 109 particles/ml, detection levels that are well within the range for viable clinical diagnostics and drug nanoparticle monitoring. DNA stained materials could also be detected directly in blood from patients with Chronic Lymphocytic Leukemia (CLL). HC-DEP sets the stage for new “seamless” sample to answer diagnostic systems which will allow a variety of important nanoscopic biomarkers and drug delivery nanoparticles to be rapidly isolated and analyzed from clinically relevant amounts of complex un-diluted biological samples.

Nov 16, 2010 Clark Center, Room S361


Jan Schnitzer, M.D. 
President and Director
Proteogenomics Research Institute for Systems Medicine (PRISM)

In vivo Proteomic Imaging of Endothelium and Caveolae for Targeted Penetration into Lung and Solid Tumors 

Hundreds of disease biomarkers have been discovered. Accomplishing noninvasive targeted imaging and nanodelivery using biomarkers is challenged by in vivo barriers limiting access inside most tissues. For example, vascular endothelium prevents the penetration of intravenously injected biological agents and nanoparticles into tissue where they can be effective. By integrating tissue subfractionation, subtractive proteomics, bioinformatic interrogation, antibody generation, expression profiling, and various imaging modalities, we can identify and actually validate the subset of biomarkers that are targetable in vivo. Tissue microenvironment extensively influences endothelial expression. Antibodies to select endothelial and caveolar proteins can not only very rapidly target a specific organ or tumor in vivo but also penetrate deep into the tissue. This greatly enhances the targeting of drugs, nanoparticles, gene vectors, and radioisotopes to facilitate disease imaging and treatment. Our "organellar proteomic imaging" strategy creates a unique delivery system with many clinical opportunities to diagnose and treat a wide variety of diseases. 

Dec 14, 2010 CISX 101 Auditorium

Luke Lee, Ph.D.
Lloyd Distinguished Professor Dept. of Bioengineering
Biomolecular Nanotechnology Center
Berkeley Sensor & Actuator Center
Univ. of California, Berkeley

Satellite Nanoscopes for Living Cell Imaging and Gene Regulation 

Biologically inspired nanosatellites are created to target, capture spectroscopic images of molecules in living cells, on-demand gene delivery, and gene regulations. Quantized Plasmon Resonance Energy Transfer (PRET)-based biophotonics provide a solution for electronic state spectroscopy of proteins in living cells. Since understanding gene function and regulation are the foundation of biology and medicine, it requires nanoscale precision controls, measurements, and experiments in live cells and organisms. For molecular optogenetic experiments in living cells, we have developed Oligonucleotides on a Nanoplasmonic Carrier Optical Switches (ONCOS) to control gene regulation and protein expression. ONCOS allows on-demand gene silencing with nanometer-scale spatial resolution and localized temperature modulation in living cells. Nanobiophotonic molecular ruler is also accomplished to measure the dynamics of enzymes, DNA, and RNA-protein interactions. 

Sponsored by: Center for Cancer Nanotechnology Excellence Focused on Therapy Response (CCNE) Program - NIH/NCI U54 (MIPS);

Host: Director, Sanjiv Sam Gambhir, MD, PhD (sgambhir@stanford.edu)

If you would like to be included on the MIPS email distribution list for weekly meeting reminders, contact Billie Robles.