BE Seminars & Events

Current Seminar Series: 2014-2015

Bioengineering Seminars are held on Thursdays from 12:00-1:00 pm unless otherwise noted. For all Penn Engineering events, visit the Penn Calendar.

Tuesday, September 9, 1:30 p.m.
BE/GABE seminar
Sheldon Weinbaum
CUNY Distinguished Professor of Biomedical & Mechanical Engineering, The City College of New York
"Changing the Odds for URM Students in STEM Disciplines Through a New Approach to Mentoring"   
Location: 337 Towne Building
Read the Abstract

34% of all 18 to 24 year olds in the U.S. are federally defined underrepresented minorities (URM). This group constitutes 12% of all BS degree recipients in engineering in the U.S. but only 8% of the B.S. degrees in BME and only 4% of the PhD's in BME. In 2002 when the BME Department was started at The City College of New York it was decided to create a department where the tenure track faculty would reflect the diversity of the undergraduate student body which was 50% URM and 50% female at the time. The fledgling department was also awarded one of two grants from NIH whose goal was to encourage URM undergraduates to purse graduate education in a life science and potentially a PhD. This grant which was renewed in 2007 and ended in the summer of 2013 has played a pivotal role in shaping the future of the department. Of particular importance in the retention of students was a novel mentorship program in which every undergraduate NIH Minority Scholar was matched with a PhD student who met with them on a weekly basis for their entire stay at the college from freshman to graduation. Virtually every PhD student and faculty member in the department was involved in some way with an NIH Minority Scholar. This interaction had a remarkable effect on faculty recruitment whose diversity today is singular among all major STEM departments in the U.S. Currently 57% of the tenure track faculty in BME are female (43%) and or URM (36%), and 70% of the PhD students are female and/or URM. For the past nine years the department has also had highest teaching evaluation in the Grove School of Engineering. This talk will tell the story of how this happened.

September 11
Xiaoyuan (Shawn) Chen
Senior Scientist, Laboratory of Molecular Imaging and Nanomedicine, National Institutes of Health
"Nanoparticle Platforms for In Vitro diagnostics, In Vivo Imaging and Drug/Gene Delivery"
Location: 337 Towne Building
Read the Abstract

Nanoparticles with unique physical and chemical properties can be rendered water-soluble and biocompatible for use in cancer diagnosis, imaging and therapy. This talk will highlight some of the recent advances in the following four areas: 1) application of materials in improving the sensitivity of biomarker detection; 2) use of different nanomaterials (both rigid inorganic materials and biodegradable polymeric materials) for multimodality imaging (PET, optical, MRI, photoacoustic, etc); 3) drug and gene loaded nanomaterials for cancer therapy; and 4) theranostic nanoplatforms with both imaging and therapeutic components combined. The challenges and future perspectives of nanomedicine in cancer research will also be discussed.

October 2
Aaron Wheeler
Associate Professor, Department of Chemistry, University of Toronto
"Digital Microfluidics for Three Dimensional Cell Culture and Single-Cell Signaling Assays"
Location: 337 Towne Building
Read the Abstract
Digital microfluidics is an alternative to microchannels for fluid handling in which discrete droplets are manipulated electrodynamically on the surface of an array of electrodes covered with a hydrophobic insulator. In this talk, I will describe two projects in which we are exploiting unique attributes of digital microfluidics to enable mammalian cell culture and analysis. In the first project, we have developed a system for generating arrays of microgels “on-demand” with arbitrary shapes and contents. We have used this system to identify conditions that control 3D kidney epithelial spheroid formation. In the second project, we have developed a system that allows for quantitative assays for single cells in situ. We have used this system to screen for PDGF signaling events with high time resolution. These examples are representative of interesting new possibilities for cell culture and analysis that are enabled by digital microfluidics. I will conclude by briefly reviewing our efforts to make these possibilities accessible to all users via open-source hardware and rapid prototyping techniques.
Seminar-Netoff

November 13
Theoden Netoff
Associate Professor of Biomedical Engineering, University of Minnesota

"Optimizing Deep Brain Stimulation for Epilepsy and Parkinson's Disease"
Location: 337 Towne Building

Read the Abstract

Deep brain stimulation (DBS) has been used for treating Parkinson's Disease with great success and somewhat lesser success for epilepsy.The mechanism by which DBS works is not well understood and thus limits our ability to really tune stimulation to maximize benefits.In this talk I will discuss theoretical approaches to understand how pathological neural activity is generated in these diseases and approaches to optimize DBS therapy.

Seminar-Kovacevic November 20
BE/ESE Seminar
Jelena Kovacevic
David Edward Schramm Professor and Head, Department of Electrical and Computer Engineering, Carnegie Mellon University
“Problems in Biologic Imaging: Opportunities for Signal Processing.”
Location: 337 Towne Building
Read the Abstract
In recent years, the focus in biological sciences has shifted from understanding single parts of larger systems, sort of vertical approach, to understanding complex systems at the cellular and molecular levels, horizontal approach. Thus the revolution of "omics" projects, genomics and now proteomics. Understanding complexity of biological systems is a task that requires acquisition, analysis and sharing of huge databases, and in particular, high-dimensional databases. Processing such huge amount of bioimages visually by biologists is inefficient, time-consuming and error-prone. Therefore, we would like to move towards automated, efficient and robust processing of such bioimage data sets. Moreover, some information hidden in the images may not be readily visually available. Thus, we do not only help humans by using sophisticated algorithms for faster and more efficient processing but also because new knowledge is generated through use of such algorithms. The ultimate dream is to have distributed yet integrated large bioimage databases which would allow researchers to upload their data, have it processed, share the data, download data as well as platform-optimized code, etc, and all this in a common format. To achieve this goal, we must draw upon a whole host of sophisticated tools from signal processing, machine learning and scientific computing. I will address some of these issues in this presentation, especially those where signal processing expertise can play a significant role.
Plaxico

December 11
Kevin Plaxco
Professor of Chemistry and Biochemistry, University of California - Santa Barbara

"Stealing Nature's Tricks to Build Better Biosensors"
Location: Berger Auditorium **PLEASE NOTE LOCATION CHANGE**

Read the Abstract
Recent years have seen the development of a broad class of optical and electrochemical sensors in which the binding of a specific molecular target is signaled via a large-scale conformational change in a protein- or nucleic-acid-based receptor. The reagentless, rapidly reversible nature of this signaling mechanism supports continuous, real-time measurement of a wide variety of analytes, and, when coupled to electrochemical read-outs, its extraordinary selectivity allows this detection to be performed in even the most grossly complicated samples, such as flowing, undiluted blood serum. Like all processes reliant on single-site binding, however, these sensors still suffer from two potentially significant limitations: the useful dynamic range of single-site receptors is centered at a fixed target concentration (defined by the receptor’s dissociation constant) and spans a fixed width (defined by the hyperbolic shape of the Langmuir isotherm). In this talk, I describe the various mechanisms that evolution has invented in order to circumvent these very same limitations (e.g., allostery, cooperativity, etc.), and demonstrate their value in improving the utility of a wide range of artificial biosensors.
  January 8
Epigenetics Seminar (tentative)
Location: 337 Towne Building
Read the Abstract
Content TBD
Plaxico

January 22
Jané Kondev
Professor of Physics, Brandeis University

"How Cells Control the Size of Their Organelles"
Location: 337 Towne Building

Read the Abstract
The cell is not a bag of chemicals. Instead it's various functions are spatially segregated in micron-sized compartments. For example, the nucleus stores and processes genetic information while the cytoskeleton provides tracks for intracellular transport. The size of these and other organelles is often under precise control by the cell. In this talk I will consider the limitations that physics imposes on simple mechanisms of size control based on a limited pool of diffusing components. In light of these theoretical results I will discuss recent experiments on actin cables in yeast that reveal the mechanism by which their lengths are controlled.
Elisseeff

January 29

Grace Hopper Lecture

Jennifer Elisseeff
Jules Stein Professor, Biomedical Engineering, Johns Hopkins University
Glandt Forum, Singh Center

Read the Abstract

Biomaterials have evolved over recent decades; transitioning from stealth implants that hide from the body to tools with biological functions that interact with and manipulate their surrounding environment. Biomaterials are the building blocks for scaffolds that direct cell and tissue function for applications in regenerative medicine. Regenerative medicine aims to rebuild and repair tissues in the body lost due to trauma, disease or congenital abnormalities. Our scaffold design centers on synthetic and biologically-derived polymers that are combined to produce biomaterials with controlled physical and physiological properties. The lecture will discuss the continuum of the biomaterials development and translation process from biomaterial structure-cell function correlations to clinical translation in cartilage and soft tissue repair.

Ferris February 5
Daniel Ferris
University of Michigan
Location: 337 Towne Building
Read the Abstract
Abstract: Although neuroscientists have been studying human brain activity for decades, they typically examine humans sitting or laying in very constrained environments performing relatively simple tasks. To better understand how the human brain works in everyday life, it is necessary to examine brain activity during unconstrained natural behaviors such as locomotion. Recent advances in hardware and signal processing techniques now allow for the examination of human brain activity during walking and running, albeit with some limitations. This seminar will present current state of the art techniques in mobile brain imaging using high-density electroencephalography combined with independent component analysis and source localization. Ongoing research in the University of Michigan Human Neuromechanics Laboratory has been able to identify electrocortical activity in specific brain regions related to the control of human walking and to performing of cognitive tasks during walking in real world environments.
Schneider-Mizell

February 6
Complex Systems Seminar Series
Casey Schneider-Mizell
Postdoctoral Researcher
Cardona Lab, Janelia Research Campus
Location: 337 Towne Building

Read the Abstract
Abstract: Multisensory integration requires neurons that receive input from distinct sensory modalities, which can occur early or late in sensory processing. However, completely mapping multisensory pathways from level to level and their behavioral relevance is difficult, as such a circuit can span widely distributed areas of the brain. In the larva of Drosophila melanogaster, we discovered that a vigorous escape behavior in response to nociceptive stimulus is enhanced by adding mechanosensory stimulus. Exploiting the larva's population of identifiable neurons with stereotyped connectivity to analyze the same circuitry across many individual animals, we dissected this circuit from first order interneurons to a single command neuron using a combination of electron microscopy (EM),  automatic behavioral quantification, and targeted genetic perturbations. Using a serial section EM volume of the entire 10,000 neuron central nervous system of the larva, we reconstructed the anatomy and synaptic connectivity of all synaptic partners of both sensory modalities and those of specific interneurons confirmed by genetic perturbation experiments to be involved in the escape behavior. In our wiring diagram of approximately 380 neurons, we found that information from the two modalities converges at the very first synapse within the nervous system, but that same unisensory and multisensory modalities also converge again and again at deeper processing layers. This suggests that multisensory integration is not a simple phenomenon that occurs at a single processing level, but a distributed computation with distinct multisensory features computed at different processing layers. Following on the use of the wiring diagram in the functional understanding of C. elegans, this work lays the groundwork for understanding whole-animal structure/function relationships from synapse to behavior in the compact yet complex insect brain.

 
Tarjei February 12
Tarjei Mikkelsen
Broad Institute, Cambridge, MA
Location: Room 9-146, Smilow
Read the Abstract
Abstract: Site-directed mutagenesis is a powerful tool for elucidating the relationship between the primary sequences and biological activities of genes and their regulatory elements. Its application has traditionally been limited by inefficient methods for generating mutant libraries, but the rapidly decreasing costs of DNA synthesis and sequencing are removing this barrier. I will describe ongoing projects that demonstrate the use of multiplexed DNA synthesis and sequencing for sequence-activity mapping with high throughput and resolution. For protein-coding sequences, we conduct pooled screens of libraries containing all possible amino acid substitutions at all positions in order to 1) guide interpretation of clinical sequencing data, 2) identify potential drug resistance alleles, and 3) guide protein engineering and synthetic biology efforts. For non-coding sequences, we use massively parallel reporter assays (MPRA) to study tens of thousands of regulatory element variants in multiple cell states, with a focus on identification of causal alleles underlying expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) hits.
Constable February 19
R Todd Constable, Ph.D.
Professor Diagnostic Radiology and Neurosurgery
Director MRI Research
Yale University School of Medicine
"Relating resting-state fMRI connectivity to behavior"

Location: Towne 337
Read the Abstract
Abstract: This talk will cover a number of recent developments in approaches to functional connectivity analysis of fMRI data describing issues and solutions to relating fMRI connectivity profiles to behavior. The use of connectivity profiles for prediction of behavior (fluid intelligence) will be shown. Both voxel based and node based connectivity analyses will be covered and their application to group and individual characteristics described. The talk will also focus on individual differences in functional connectivity and the potential of functional phenotyping.
  February 26
Heike Daldrup-Link
Stanford University
Location: 337 Towne Building
Read the Abstract
Content TBD
Yang March 5
Fan Yang
Stanford University
"Engineering Stem Cells from "Outside-In" and "Inside-Out": A Biomaterials-mediated Approach"
Location: 337 Towne Building
Read the Abstract
Abstract: Stem cells are attractive cell sources for regenerative medicine due to their unique capacity of differentiation, as well as their ability to contribute to tissue repair via paracrine signaling. However, the efficacy of applying stem cells alone to achieve robust tissue regeneration in situ remains limited, often due to lack of appropriate microenvironmental cues to guide desirable cellular fates. In this talk, I will discuss examples of our research on how to employ biomaterials to address these challenges using two strategies. In the first strategy, we engineer stem cell microenvironments from “outside-in” by developing novel biomaterials as artificial extracellular matrix. Using a “lego-building” approach, our platforms allow fabrication of biomaterials modules with independently tunable cell niche properties including biochemical, mechanical and topographical cues. Such biomaterials can provide useful tools to enhance cell engraftment, guide desirable cell fates and provide tissue-mimicking mechanical properties. In the second strategy, we harness stem cells as drug delivery vehicles and its ability to catalyze tissue regeneration via paracrine signaling. We can further engineer the paracrine signaling of stem cells from "inside-out" using biodegradable polymeric nanoparticle-mediated non-viral gene delivery. Potential applications of such stem cell and biomaterials-based strategies for treating musculoskeletal and cardiovascular diseases will be demonstrated using relevant animal models.

Constable March 6
Richard Betzel 
Psychological and Brain Sciences/Cognitive Science,
Indiana University
"Generative models of the human connectome"

Location: 337 Towne Building
Read the Abstract

Abstract:  The configuration of connections in the human connectome, the "wiring map" of an organism’s neural system, is thought to arise from a drive to reduce the total cost of wiring while simultaneously promoting efficient information processing. We attempted to disentangle the contributions made by these components by incorporating geometric (spatial) and topological information into the wiring rules of network generative models for the human connectome.

Across three independently acquired human MRI datasets (N=380 participants in total), we found that generative models where connection formation was based solely on spatial proximity were unable to produce realistic synthetic networks. Specifically, such models underestimate the number of long-range connections and fail to reproduce the distance-dependent degree assortativity that characterize empirical human connectomes.

On the other hand, models whose wiring rule included both spatial and topological information were able to match these properties and others. Of this class of models, we found that the best-fitting model combined a topological parameter for homophily, calculated as the similarity of connectivity profiles, and a geometric parameter that penalized the formation of long-distant connections. Fitting these models to the connectomes of a cohort whose ages ranged from 7-85 years, we find that the homophily parameter remains constant with age, whereas there was a monotonic reduction of the geometric parameter, suggesting that “older” networks penalize long-distance connections proportionally less.

Stone March 12
Howard Stone
Princeton University
"At the intersection of (fluid) mechanics and molecular biology"

Location: Berger Auditorium
Read the Abstract
We provide several examples of unexpected effects that occur with bacterial systems in the presence of fluid motion, which is representative of their natural environment. In one case we document how surface-attached bacteria capable of twitching motility, which is normally associated with random bacterial movements on a surface, can lead to bacteria migrating upstream opposite the direction of flow. We highlight how such motions might lead to unanticipated spreading of bacterial in porous networks. In a second example, we provide evidence that flow can help rationalize the shape of the curved bacterium Caulobacter crescentus. Finally, we investigate some influences of flow on biofilms. In particular, we identify the formation of biofilm streamers, which are filaments of biofilm extended along the central region of a channel flow, and show how these filaments are capable of causing catastrophic disruption and clogging of industrial, environmental and medical flow systems. A feature that recurs throughout the talk is the interplay between flow and the bacterial system.
Manalis March 19
Scott Manalis
Massachusetts Institute of Technology
"Measuring Single Cell Growth and Response to Targeted Cancer Therapies"
Location: 337 Towne Building
Read the Abstract
Despite significant advances in our understanding cancer genetics, patients often receive empiric treatments with nonspecific cytotoxic therapies. Better information about which treatment to offer an individual patient (i.e., precision medicine) could improve efficacy while sparing patients from the toxicity of therapies that offer no benefit. My laboratory is developing an approach where physical measurements of single cells (mass and growth rate) are used together with flow cytometry to isolate and characterize phenotypically resistant subpopulations within human tumors.  Together with collaborators at the Dana Farber Cancer Institute, we aim to provide a unique opportunity to define the architecture of drug response across heterogeneous tumor populations, to characterize minimal residual disease specimens, and ultimately to predict in situ response within a timeframe conducive to clinical decision-making. 
Macklin March 20
Dr. Christopher Macklin
University of Illinois School of Music
"Follow your ears: Music and Scientific Problem Solving from Euler to EEGs"
Location: 337 Towne Building
Read the Abstract
One way of defining music is as a frame through which the relationships between sounds acquire meaning. Musical thinking is thus not an exclusive activity reserved to those who choose to manipulate sound through instruments such as violins and pianos, but instead is a state of mind open to any who choose to approach a situation “ears first.” Though often seen as a hallmark of 20th century modernist classical music-making, this kind of sonic lens on the world has long been an important tool of natural philosophers and scientists, and in the past 30 years an ever-increasing number of applications have been found for novel approaches to sonifying elements of complex data sets. In this talk, Christopher Macklin (a neuroscientist-turned-music historian) will discuss some of the ways that musical thinking and scientific innovation have intersected in the work of figures such as Leonhard Euler and Alvin Lucier, and highlight some of the ways that modern researchers are applying musical models to understanding the dynamics of coupled systems such as neural networks and protein assemblies.
Keilhoz March 25
Sheila Keilhoz
Georgia Institute of Technology and Emory University School of Medicine
"What's in the BOLD Signal? Neural and Non-neural Contributors to Functional Connectivity and Resting State MRI"
Location: 337 Towne Building
Read the Abstract
New resting-state MRI acquisition and analysis techniques are making it possible to obtain information about network dynamics in the brain.  The patterns of changing network connectivity have been linked to fluctuations in simultaneous electrical recordings in healthy humans and anesthetized animals.  Based on these initial studies, we hypothesize that at least two independent processes contribute to the resting-state MRI signal.  The first is a quasiperiodic, large-scale spatiotemporal pattern that appears to arise from very low frequency (< 1 Hz) electrical activity and has plausible links to attention and vigilance.  The second process consists of irregular changes in the connectivity between selected areas.  It is linked to variation in the correlation of high frequency power, particularly in the beta and gamma bands, and we speculate that these changes may be more closely linked to cognitive processes.  If our hypothesis proves true, we may be able to separate out the relative contributions of these two sources to the MRI signal, with the goal of obtaining more sensitive indices of cognitive changes along with quantifiable monitoring of attention and vigilance.
 

April 2
Kwabena Boahen
Stanford University
Location: 337 Towne Building

Read the Abstract
Content TBD
Spivak

Friday, April 3 at 10 a.m.
Complex Systems Seminar Series

David Spivak, Department of Mathematics
Massachusetts Institute of Technology
"Thinking about modularity in networks"
Location: 337 Towne Building

Read the Abstract

The word "modular" describes situations in which multiple parts can be arranged, based on their interfaces, to form a larger whole. Often this idea can be repeated, so that the new whole can be considered one part in an even larger whole; in this way we can continually zoom out. For example, if one puts an interface on a network N---considering some nodes of N external and others internal---then N can be represented as a single node in a larger network system. By zooming out, the dynamics taking place inside the network N have been abstracted as the internal state of the representing node.

There is something like a new arithmetic, which I might call operadics, for thinking about the kind of modular situation described above. Operadics is the theory of operads, a subfield of category theory designed to capture the abstract notion of "operation". Operadics is not much more difficult than arithmetic, nor is it much more powerful; it's the basics, the foundation. As a mathematical framework, its purpose is to serve as solid, rigorous ground on which to think clearly about the issue of modularity, i.e., about how systems come together to form larger systems.

I will describe this new arithmetic of modularity from the ground up, focusing on examples. In particular, I will assume no mathematical background other than sets, functions, and their compositions, as well as the ability to parse mathematical notation, such as f: A-->B.

  April 9
Tammy Haut Donahue
Colorado State University
Location: 337 Towne Building
Read the Abstract
Content TBD
  April 16
Steven George
University of Colorado
Location: 337 Towne Building
Read the Abstract
Content TBD
 

April 23
Herman Schwan Lecture

Samuel Stupp
Board of Trustees Professor of Materials Science and Engineering, Chemistry, and Medicine; Professor of Biomedical Engineering; Northwestern University
Location: 337 Towne Building; Please note the change in time to 3 PM

Read the Abstract
Content TBD
  May 14
Epigenetics Seminar (tentative)
Location: 337 Towne Building
Read the Abstract
Content TBD
  June 11
Peter Fraser
The Babraham Institute
Location: 337 Towne Building
Read the Abstract
Content TBD