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STMC-sponsored Seminars

The STMC leadership encourages all STMC students, fellows and members to invite and host seminar speakers whose research is aligned with STMC interests. Cosponsorship with other departments and centers is also strongly encouraged. See "procedures for coordinating seminars" for directions on hosting a speaker.

2012

Tuesday, APRIL 24
"Mitochondrial Membrane Dynamics and ER Rab GTPases"
Dr. Thomas Simmen, University of Alberta
April 24, 2:00 PM in CRF 204

Host: Angela Wandinger-Ness

Dr. Simmen has identified the function of Rab32, which was shown to have an unusual mitochondrial localization. He has discovered that Rab32 plays a central role in intracellular calcium signaling, apoptosis and mitochondrial ATP production. He is also interested in mechanisms that are relevant to cancer (based on the discovery of a novel tumor suppressor) and neurodegeneration related to MS and Parkinsons.

Friday, MARCH 23
"TNF ligand binding and receptor network formation: Exploring structure and function"
Christopher C. Valley
Postdoctoral Candidate
12:00 PM, CRF 204

Monday, MARCH 19
"Development rooted in interwoven networks"
Philip Benfey
Director, Duke Center for Systems Biology
4:00 - 5:00 PM, CRF 204

Friday, MARCH 16
Guest Speaker: Toshi Kawakami
La Jolla Institute of Allergy & Immunology
12:30: Luncheon 1:00-2:00: Toshi Kawakami

Monday, MARCH 05
Talk: "Quantification of Collagen Alignment: Tools for Characterizing Cancer Invasion and Progression"
Carolyn Pehlke
University of Wisconsin
4:00 - 5:00 PM in CRF 204

Thursday, JANUARY 19
"The Role of Microstructural Polymorphisms in Class I HLA-B Peptide Binding"
Molecular Genetics Pathology Fellow
Ramachandra Gullapalli, MD, PhD
Division of Molecular Diagnostics, Department of Pathology
University of Pittsburgh Medical Center
Pittsburgh, Pennsylvania
8:00 AM
BMSB Room 303
Download Ramachandra Gullapalli CV

2011

Thursday, DECEMBER 01
Rick Kahn, Emory University

Friday, OCTOBER 07
Michael J. Saxton
Dept of Biochemistry and Molecular Medicine
University of California
10:00 AM
CRF-G25

"Move, dither, move, dither. On the structure of normal and anomalous random walks and single-particle trajectories"

Abstract: The fundamental principle in interpreting single-particle trajectories is that a pure random walk is the control and null hypothesis. In order to make any claim about any physical or biological event in an observed single-particle trajectory, one must evaluate the probability that the event could have occurred by chance in the corresponding pure random walk. By eye, a random walk often shows alternating periods of "moving" and "dithering." We quantify this apparent structure by Monte Carlo calculations of pure random walks in which various measures of apparent directed motion ("moving") and apparent confinement ("dithering") are compared. We also compare normal random walks with fractional Brownian motion, in which the dithers are denser and more prolonged, and the moves are much shorter.

Monday, SEPTEMBER 26
James Werner
Technical Staff Member, Los Alamos National Laboratory
2:30 PM
Rm. #101, Center for High Technology Materials (CHTM)

"Time-Resolved Three-Dimensional Molecular Tracking and New Fluorescent Probe Development"

Abstract: Our lab has developed a method for tracking individual quantum dot (QD) labeled proteins as they move in 3D inside of live cells. Our method uses four overlapping confocal volume elements and active feedback once every 5 ms to follow three-dimensional molecular motion. We have recently used this instrument to follow individual QD-labeled signaling molecules (IgE-FceRI) on and inside living cells. During later stages of the signal transduction cascade, clusters of QD labeled molecules were captured in the act of ligand-mediated endocytosis and tracked during rapid (950 nm/s) vesicular transit through the cell.

In addition to 3D tracking, our lab is quite interested in new fluorescent probe development. In particular, we have developed a new DNA detection probe based upon fluorescent nanoclusters of a handful of atoms of silver or gold. This new probe, termed a NanoCluster Beacon (NCB), "lights-up" tremendously (~200 fold brighter) upon binding target DNA.

Thursday, SEPTEMBER 08
Reinhard Laubenbacher, PhD
Virginia Bioinformatics Institute
10:00 AM
Harvey Library (BMSB 309)
Download Map to Harvey Library

"Cancer Systems Biology"

Abstract: Our understanding of cancer has been aided by a network centric view. The fundamental relevance of systems biology to the understanding and treatment of cancer is the insight that genes and proteins do not act in isolation, but rather as nodes in complex interactive networks that include multiple feedback mechanisms and redundancies. The design of effective drugs to battle cancer will depend on the understanding of these networks and of the specific network alterations present in an individual tumor. And an understanding of characteristic changes in metabolic networks can lead to new prognostic and diagnostic methods. The complexity of these dynamic networks makes it difficult or impossible to study them without the aid of computer models based on mathematical analysis. This talk will discuss systems biology and mathematical models as an approach to cancer biology by way of two case studies. One of these focuses on our research on intracellular iron metabolism and its relationship to breast cancer.
http://www.vbi.vt.edu/faculty/personal/Reinhard_Laubenbacher

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Wednesday, SEPTEMBER 07
Dr. Olena Ivashyna
Dr. Wickline's laboratory
Washington University
St. Louis, Missouri
12:00 PM
CRF 204

"FCS study of the pore formation by the human protein Bax in lipid membranes."

Tuesday, SEPTEMBER 06
Michelle N. Archuleta, PhD
Post-Doctoral Fellow
Computational Biology & Bioinformatics Group
Pacific Northwest National Lab
Richland, WA
2:00 - 3:00 PM
CRF 204

"Studying innate immunity signaling mechanisms: What lessons can we learn from pathogens and particles?"

Abstract: The innate immune system is our first line of defense against pathogens and foreign materials. Salmonella, a major contributor of food borne illness, is an excellent model for understanding host-pathogen interactions as many of its virulence strategies are well characterized. At the other end of the spectrum inert nanoparticles have been shown to elicit an immune response that is dependent on size and functionality. Our ability to determine the underlying mechanisms that link genotype to phenotype for innate immune response and host pathogen interactions will rely on our ability to leverage experimental measurements with mathematical models. Understanding innate immunity from the prospective of a pathogen, Salmonella and inert nanoparticles this talk will focus on two different approaches used in systems biology both integrate experimental data and prior knowledge of the biological system. I will describe a bottom-up approach using ordinary differential equations and uncertainty quantification to develop a mathematical model of TLR4 signaling from a priori knowledge of the literature and refining the model with experimental measurements. In addition I will describe some sophisticated Monte Carlo algorithms that I have developed for resolving spatio temporal scales of signal transduction pathways that take advantage of adaptive coarse graining. Taking a top-down approach, I will describe some bioinformatics and multivariate regression algorithms for deriving time-dependent relationships from high throughput 'omics' measurements of macrophages exposed to inert nanoparticles. The underlying theme of this work emphasizes the need to merge biological measurements with novel algorithms and computation in order to understand innate immune signaling and host pathogen interactions.

Thursday, SEPTEMBER 01
Pavel Kraikivski, PhD
Postdoctoral Fellow
Center for Cell Analysis and Modeling
University of Connecticut Health Center
10:00 - 11:00 AM
Fred Harvey Library (BMSB 309)
Download Map to Harvey Library

"Diffusion in Cytoplasm: Effects of Excluded Volume Due to Internal Membranes and Cytoskeletal Structures"

Abstract: The interior of the cell is filled with cytoskeletal networks and intracellular membranes with intricate geometry. Thus the space available for diffusion in cytoplasm is convoluted and macromolecule diffusivity is affected as a consequence of increase in a path length, sometimes termed as 'the effect of excluded volume'. I will present a systematic computational study of this effect by approximating intracellular structures as mixtures of random overlapping obstacles of various shapes. Three-dimensional simulations of Brownian motion in the entangled filament networks reveal the anomalous time dependence of a particle mean squared displacement on the time and spatial scales determined by the ratio of a particle radius and the network mesh size. This is consistent with the experiments with tracer particles and with earlier modeling studies of diffusion on lattices. On a sufficiently large spatial scale, at which the medium can be considered as homogeneous, the diffusion becomes normal. Effective diffusion coefficients are computed using a fast homogenization technique. It is found that a simple two-parameter power law provides a remarkably accurate description of effective diffusion over the entire range of volume fractions and for any given composition of structures. This universality allows for quick estimation of diffusion coefficients, and also void percolation thresholds once the obstacle shapes and volume fractions are specified. It is estimated that the excluded volume effect alone can account for a four-to-six fold reduction in diffusive transport in cells, relative to diffusion in vitro. The study lays the foundation for an accurate coarse-grain formulation that would account for cytoplasm heterogeneity on a micron scale and binding of tracers to intracellular structures.
Hosts: Drs. Janet Oliver, Regents' Professor, Project Director STMC & Bill Hlavacek

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Wednesday, JULY 27
Dr. Rob J. De Boer
Theoretical biology
Utrecht University

Wednesday, July 27, 2011
Room 100, Castetter Hall
12:00 PM

"Analysing immune cell migration"

The visualization of the dynamic behaviour of and interactions between immune cells using time-lapse video microscopy has an important role in modern immunology. To draw robust conclusions, quantification of such cell migration is required. This is far from trivial because imaging experiments are associated with various artefacts that can affect the estimated positions of the immune cells under analysis, which form the basis of any subsequent analysis. We construct spatially explicit models of T cell and DC migration in LNs and show that several dynamical properties of T cells are a consequence of the densely packed LN environment. Our three-dimensional simulations suggest that the initial decrease in T-cell motility after antigen appearance is due to "stop signals" transmitted by activated DCs to T cells. Because imaging is typically restricted to experiments lasting 1 h, and because T cell-DC conjugates frequently move into and out of the imaged volume, it is difficult to estimate the true duration of interactions from contact data. We propose a method to properly make such an estimate of the average of the contact durations. The method is validated by testing it to our spatially explicit computer simulations. We use these techniques to analyze the migration of antigen specific CD8 T cells in the skin after localized infection with herpes simplex virus.

Thursday, JULY 07
"When Worlds Collide: The impact of focal adhesions on leukocyte trafficking"
Kamala D. Patel, PhD
Professor, University of Calgary

Thursday, July 07, 2011
Fred Harvey Library (BMSB 309)
11:00 AM - 12:00 PM

Wednesday, JUNE 29
CANCER MODELING SEMINAR
"Temporal Evolution of Cancer Risk"

Suresh Moolgavkar, MD, PhD
Professor of Epidemiology, Hutchison Cancer Center, Seattle
Adjunct Professor of Applied Mathematics, University of Washington

UNM Cancer Center
11:30 -12:00: Lunch in Cancer Center Foyer
12:00 - 1:00: Lecture in UNM Cancer Center Auditorium
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Relevance: Dr. Moolgavkar's research integrates the fields of epidemiology, biostatistics, and quantitative risk assessment. He is internationally known for his work in developing mechanistically based dose-response models for carcinogenesis, and, in particular, for the two-mutation clonal expansion model, also known as the Moolgavkar-Venzon-Knudson (MVK) model.

Friday, MAY 06
BIOLOGICAL PHYSICS COLLOQUIUM
William E. Balch
Departments of Cell Biology and Chemical Physiology, The Skaggs Institute for Chemical Biology, The Institute for Childhood and Neglected Disease, The Scripps Research Institute (TSRI), La Jolla, CA
4:00 PM
Dane Smith Hall, Room 125
Title: Balancing the Biophysics and Biology of Protein Folding to Manage Human Healthspan
The cell exploits the emergent properties of general proteostasis, a biological system of folding chaperones, degradation systems and folding stress-responsive signaling pathways of high clinical relevance, to manage human biology (Science (2008) 319:916; Curr. Opin Cell Biol (2011) 23:126). The proteostasis network generates and maintains proteome balance inside and outside diverse cell, tissue and organ environments in the germline, during development and in response to disease and aging (Science (2010) 367:766; Nature (2011) 471:42). Physical, pathological and inherited challenges to the basic biophysics (the energetics) of the biological fold can compromise proteome balance. By the use of systems-level proteomic, genomic and bioinformatic tools, we are building a dynamic, multi-layered view of the healthy biological protein fold and the changes that occur in response to energetically compromised folding stress such as is observed in neurodegenerative disease, diabetes, COPD / emphysema, cancer and cystic fibrosis. We are finding that chemical biology management of the proteostasis network can alter the composition of the local proteostasis program to restore function across a broad spectrum of human disease. The discovery of tools that redirect the activity of biological folding systems highlights the potential value of the dynamic emergent properties of the proteostasis network to therapeutically rebalance the proteome to benefit human healthspan.

Thursday, APRIL 28
Vittorio Cristini, PhD
Professor, Departments of Pathology and Chemical and Nuclear Engineering
"Multiparameter Computational Modeling of Tumor Invasion"
3:30 PM
SMLC (Science and Math Learning Center) Room 356
The SMLC is Building #14, J-15 on the Grid of the UNM Central Campus Map
Abstract: Clinical outcome prognostication in oncology is a guiding principle in therapeutic choice. A wealth of qualitative empirical evidence links disease progression with tumor morphology, histopathology, invasion, and associated molecular phenomena. However, the quantitative contribution of each of the known parameters in this progression remains elusive. Mathematical modeling can provide the capability to quantify the connection between variables governing growth, prognosis, and treatment outcome. By quantifying the link between the tumor boundary morphology and the invasive phenotype, this work provides a quantitative tool for the study of tumor progression and diagnostic/prognostic applications. This establishes a framework for monitoring system perturbation towards development of therapeutic strategies and correlation to clinical outcome for prognosis.

Thursday, APRIL 07
Johannes Huppa, PhD
Research Associate, Department of Microbiology and Immunology
Stanford University Medical School
"How T cells Detect Antigens - a Molecular Imaging Approach"
9:30 AM
Fred Harvey Library (BMSB Room 309)

Tuesday, MARCH 22
Hans G. Othmer, PhD
School of Mathematics & Digital Technology Center
University of Minnesota, Minneapolis, MN
Title: Multiscale Modeling in Biology — The question is — What is the Question?
Abstract: The complexity of signal transduction and gene control networks poses many challenges for modeling and analysis, particularly when we try to translate molecular and cell-level information to organ or organism-level descriptions. As a result it is important to focus clearly on what question is to be addressed and choose the appropriate level for modeling accordingly. We will illustrate this with a number of examples ranging from pattern formation in embryogenesis to hybrid models for tumor growth, and will discuss some of the open problems in this area.
10:00 AM
CRF 204
Visit: http://www.math.umn.edu/~othmer/

Thursday, MARCH 10
Jiyun Kim, MD, PhD
Research Scientist, Skirball Institute, Molecular Pathogenesis Program
NYU School of Medicine
"Ins and outs of breaking the blood brain barrier"
9:30 AM
Fred Harvey Library (BMSB Room 309)

Monday, FEBRUARY 28
Aaron Neumann, PhD
Research Assistant Professor, Cell and Developmental Biology
University of North Carolina at Chapel Hill
"Dendritic cell C-type lectins: Nanoscale membrane organization to mesoscale pathogen recognition"
9:00 AM
Fred Harvey Library (BMSB Room 309)

Friday, FEBRUARY 25
Cees van der Poel
Department of Immunology
University Medical Center Utrecht
"Functional characterization of the high affinity IgG receptor"
9:00 AM
CRF 204

Friday, JANUARY 28
Yi Wu, PhD
Assistant Professor, Center for Cell Analysis and Modeling
University of Connecticut Health Center
"Interrogating cellular signaling with biosensors and photoactivable proteins"
11:00 AM
Fred Harvey Library (BMSB Room 309)

Wednesday, JANUARY 26
Elaine Bearer, MD-PhD
Professor and Vice Chair for Research from the Department of Pathology
UNM-HSC
"Hitchhiking in the brain: from molecules to neurons to circuits, how does it work?"
3:00 PM
Castetter Hall (Biology Department), Room 1420 (PiBBs Suite)
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Monday, JANUARY 24
Robert Hoffman, MD
Professor of Surgery
University of California, San Diego
"The Multiple Uses of Fluorescent Proteins To Visualize Cancer In Vivo"
12:00 PM
Cancer Center Auditorium
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2010

Friday, NOVEMBER 19
Tomasz Lipniacki, PhD
Division of Modeling in Biology and Medicine
Institute of Fundamental Technological Research
Polish Academy of Sciences
Warsaw, Poland
“Activation of B-cells: Positive and Negative feedbacks and Spatial Reorganization”
1:00 PM
CRF G025

Wednesday, OCTOBER 20
Dr. Alessandra Cambi from University of Nijmegen Medical Centre will be presenting "Nanoclusters of the lipid raft-associated HIV-1 receptor DC-SIGN internalize antigens via multiple endocytic pathways"
12:00 PM
Harvey Library (BMSB 309)

Tuesday, OCTOBER 19
Dr. Maria F. Garcia-Parajo from Institute for Bioengineering of Catalonia will be presenting "Integrin nanodomains on leukocyte cell membranes"
4:00 PM
Harvey Library (BMSB 309)

Tuesday, SEPTEMBER 21
Dr. Alex Mogilner
STMC & Math Department are hosting
4:00 PM
Harvey Library (BMSB 309)
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Thursday, SEPTEMBER 16
Ian Parker, Ph.D.
"Imaging the activity and localization of individual IP3 receptor/channels in intact cells"
Professor of Neurobiology
Department of Neurobiology and Behavior
University of California, Irvine
website: http://parkerlab.bio.uci.edu
9:30 AM
Harvey Library (BMSB 309)

Wednesday, SEPTEMBER 15
Dr. John Pearson, Los Alamos National Labs
"The dynamics of endogenous calcium buffers near an ion channel"
11:00 - 12:00 PM
Room CRF 204
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