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Seminars

2017

Tuesday, MAY 16

“New Concepts for Quantifying the Benefits of Single Agent and Combination Cancer Therapies in an Era of Big Data,” Peter Sorger, Otto Krayer Professor of Systems Biology School and Director of the Laboratory of Systems Pharmacology, Harvard Medical School, Boston
UNM Cancer Center Auditorium, Noon (Lunch with STMC trainees from 11:00-11:45)

Thursday, MAY 4

“Beneficial Roles of Mast Cells and IgE: Enhancing Innate and Acquired Resistance to Venoms,” Stephen J. Galli, MD, Chair, Department of Pathology, Stanford University School of Medicine, Stanford CA.
8:00 AM, Fitz Hall 303

Tuesday, APRIL 18

“Clonal Selection in B Cell Development and Leukemia,” Markus Muschen, Chair of Department of Systems Biology, Beckman Research Institute & Associate Director NCI Comprehensive Cancer Center, City of Hope National Medical Center, Duarte CA
UNM Cancer Center Auditorium, Noon. Lunch at 11:30 am

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Friday, MARCH 31

Dissertation Defense: M. Frank Erasmus. "Validation of the pre-B Cell Receptor as a Therapeutic Target in B Cell Precursor Acute Lymphoblastic Leukemia". Mentor: Bridget Wilson
3:00 PM, Fitz Hall 303

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Thursday, MARCH 9

"What did I just see? Inference and interpretation with super-resolution microscopy," Daniel Coombs, PhD, Professor, Department of Mathematics and the Institute of Applied Mathematics, University of British Columbia, Vancouver.
4:00 PM, CRF-G25

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Monday, MARCH 6

"Single molecule bond mechanics of cadherin cell adhesion proteins", Dr. Kristine Manibog, Georgia Institute of Technology, Atlanta, GA
1:00 - 2:00 PM, CNLS Conference Room, Los Alamos National Laboratory

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Thursday, FEBRUARY 9

"Systems biology modeling to investigate signaling pathways in cancer", Stacey D. Finley, PhD, Gabilan Assistant Professor, Department of Biomedical Engineering, Department of Chemical Engineering and Materials Science University of Southern California
4:00 PM, CRF-G25

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Monday, JANUARY 23

Dissertation Defense: Ellen Hatch. "Utilizing Quantitative Fluorescence Microscopy to Study Oncogenesis". Mentor: Diane Lidke
1:00 PM, Fitz Hall 203.

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Thursday, JANUARY 19

Doreen Cantrell, University of Dundee will present "Shaping the T cell proteomic landscape by antigen receptor and cytokines".
11:00 AM - 12:00 PM, CRF G25. Host: Wilson

Professor Doreen Cantrell is a Wellcome Trust Principal Research Fellow at the School of Life Sciences, University of Dundee. Her research interests are focused on T lymphocyte development and activation, a key process to the comprehension and manipulation of mammalian immune responses. She has published over 180 research papers and was elected a Fellow of the Academy of Medical Sciences and EMBO in 2000, a Fellow of the Royal Society of Edinburgh in 2005 and a Fellow of the Royal Society in 2011. She was awarded Commander of the British Empire in the 2014 New Year Honours for her services to the UK Science. She has sat on numerous scientific committees and editorial boards and is currently a Member of the Medical Research Council, the Wellcome Trust Sir Henry Dale Fellowship Committee, a Member of the Babraham Institute Board and Trustee of The Francis Crick Institute.

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Tuesday, JANUARY 10

Dissertation Defense: Christina Termini. "CD82 Membrane Scaffolding: Regulation of Hematopoietic Cell Adhesion and Signaling"
2:00 PM, Fitz Hall 303

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Monday, JANUARY 9

"Regulation of Foxp3 expression in regulatory T cells by epigenetic modifications", Akihiko Yoshimura, Ph.D., Professor, Department of Microbiology and Immunology, Graduate School of Medicine, Keio University, Tokyo, Japan.
9:00 AM, CRF 104.

2016

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Wednesday, DECEMBER 14

Genevieve Phillips has announced her Masters defense entitled, "Developing Fluorogen Activating Protein-Fluorescent Protein FRET Pairs for Live Cell Imaging".
9:00 AM, Health Sciences & Services Building (HSSB) Room 105

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Tuesday, DECEMBER 13

Matt Graus announces his dissertation defense entitled, "Concealing Carbohydrates: Candida species Secret to Masking Beta-Glucan".
2:00 PM, Fitz Hall 303

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Friday, DECEMBER 2

"Understanding Functional Connectivity Differences in the Brain Using Functional Magnetic Resonance Imaging: Huntington's Disease," STMC Alumni Flor Espinoza, PhD, Research Scientist, The Mind Research Network
12:00 PM, UNM SMLC 356 (QuantBrains UNM/MRN Research Seminar Series)

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Thursday, DECEMBER 1

"An Introduction to Mass Cytometry: A revolution in single-cell proteomics, enabling the most comprehensive understanding of cell phenotypes, signaling pathways and function", Anita Kant, Ph.D, Field Applications Scientist, Fluidigm Corp. Please RSVP: http://info.fluidigm.com/unmmasscyto2016
4:00-5:00 PM, Cancer Research Facility, Room 204

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Thursday, NOVEMBER 10

"Robots learn from nature's flexible foragers: How T cells, ants, and robots search effectively by adapting to their environment" Melanie E. Moses, Professor, UNM Department of Computer Sciences
4:00 PM, CRF G25

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Wednesday, NOVEMBER 2

"Computational Systems Biology: Reverse engineering advanced, alien technology", Michael Brent, Department of Computer Science and Engineering, Washington University in Saint Louis
2:00 PM, Centennial Engineering Center Room 1041.

Monday, OCTOBER 17

Pedro 'Peter' Relich defense: "Single Particle Tracking: Techniques in Live Cell Nanoscopy". Mentor: Keith Lidke, PhD
2:00 PM, Physics & Astronomy Room 190.

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SEPTEMBER 8, 9, 28

Cell Authentication Workshops and Research Study: Introductory Training Session: 9-11 AM, September 8 or 9, 2016, at locations on main and HSC campuses. Optional follow-up Debriefing Session: 3-5 PM September 28, 2016. View Cell Authentication Workshops Registration Information

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Wednesday, AUGUST 10

Julia Xiaojun Zhao, PhD, Professor, Department of Chemistry, University of North Dakota
12:00 PM, CRF 204.

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Wednesday, AUGUST 10

Presentation by Beatrice David Shevlin, PhD, of the Opera Phenix and Operetta CLS High Content Imaging platforms and of scientific results obtained with PerkinElmer's HCS instruments.
2:00 PM, CRF 204.

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Tuesday, JULY 19

Comprehensive Exam: Ellen Hatch, "Molecular mechanisms and consequences of RON/EGFR crosstalk"
1:00 PM, CRF 204.

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Tuesday, JULY 12

Dissertation Proposal Defense: Kasra Manavi, "Simplified Motion-Based Simulation of Large Molecule Interactions"
10:00 AM - 12:00 PM, ECE 118.

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Thursday, JUNE 30

"Signatures of Mutational Processes in Human Cancer", Dr. Ludmil Alexandrov, Oppenheimer Fellow in the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and member of the UNM Comprehensive Cancer Center.
12:00 PM, UNM Comprehensive Cancer Center Auditorium.

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Tuesday, JUNE 14

MATLAB Clustering Classes. Presenter: Michael Wester, STMC, The University of New Mexico Health Sciences Center
3:00-5:00 PM, CRF-G25.

Tuesday, MAY 24

"Stabilization of EphA2 dimers as a novel anti-cancer strategy", Dr. Deo Singh, postdoctoral candidate in the Neumann lab.
11:00 AM, Fitz 309.

Thursday, MAY 19

"Dynamic Bayesian Network Models of Interacting Single Particle Trajectories", Dr. Mark Olah.
3:00 PM, UNM Physics and Astronomy room 1131.

Monday, MAY 16

Comprehensive Exam: Prashant Dogra. "Mathematical Modeling of Transport of Exogenous Nano-Sized Cargo in Biological Systems"
2:00-4:00 PM, CRF-G25.

Tuesday, APRIL 26

Biomedical Sciences Graduate Program: Emanuel Salazar-Cavazos, Comprehensive Exam. "Studying ErbB family homo- and heterodimer signaling through single molecule imaging and modeling". Mentor: Dr. Diane S. Lidke (UNM), Co-mentor: Dr. William S. Hlavacek (LANL)
10:00 AM, CRF-G25.

Thursday, APRIL 14

STMC short presentations. STMC's Dr. Keith Lidke presenting STMC SuperResolution Core updates and Dr. Timothy Travers, Postdoctoral Research Associate, Los Alamos National Laboratory, will present "Computational modeling of α-actinin structure and regulation".
4:00 PM, CRF-G25.

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Friday, FEBRUARY 26

Rob Phillips, Fred and Nancy Morris Professor of Biophysics and Biology, California Institute of Technology.
4:00 PM, Physics and Astronomy Building.

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Thursday, FEBRUARY 25

"Studies of the folding of globular proteins and the dynamics of membrane proteins", Angel E. Garcia, Ph.D., Director, Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory
4:00 PM, CRF-G25.

Thursday, FEBRUARY 18

"Multi-color fluorescence in-situ hybridization (M-FISH) image analysis based on sparse representation models", Dr. Jingyao Li. Dr. Li is interviewing for an STMC post-doc position.
9:30 AM in Physics room 1131.
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Thursday, FEBRUARY 4

"STMC Vignettes: Systems approaches to BCP-ALL", Bridget Wilson, Ph.D., UNM Department of Pathology & STMC director, in UNM Neurosciences Seminar Series
12:00 PM, Fitz Hall 303.

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Thursday, JANUARY 28

"Intravital Microscopy of Cancer Invasion, Metastasis and Therapy Response", Peter Friedl, M.D., Ph.D., Professor, Microscopical Imaging of the Cell, Dept. of Cell Biology, Radboudumc, Nijmegen, The Netherlands. Joint faculty: Molecular Imaging, Dept. of Genitourinary Medical Oncology, Univ. of Texas MD Anderson Cancer Center, Houston, TX
8:00 AM, Fitz Hall 203.

2015

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Friday, DECEMBER 4

Samantha Schwartz, "Visualizing Mast Cell Activation: Single Molecule Dynamics of Early Events in FcεRI Signaling", dissertation defense.
1:00 PM, Fitz Hall 303.

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Friday, DECEMBER 4

Physics & Astronomy Colloquium: Professor Rafael Piestun, University of Colorado. Hosted by STMC's Keith Lidke.
4:00 PM, Dane Smith Hall 125

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Friday, OCTOBER 23

"Regulation of the Ras oncoprotein by post-translational modification", Dr. Sharon Campbell, Professor of Biochemistry and Biophysics, UNC, Chapel Hill, NC.
12:00 PM, Fitz Hall 203

Friday, OCTOBER 16

Lecture: "High-Dimensional Nonparametric ODE Models for Dynamic Gene Regulation Networks", Tao Lu, PhD, Tenure Track Faculty Candidate, Biostatistics Shared Resource, Assistant Professor; Associate Director Statistical Consulting service, State University of New York, Rensselaer, New York.
12:00 PM, CRF G25 (lunch provided)

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Monday, OCTOBER 12

Seminar: "Alkyne-modified isoprenoid analogs enable global analysis of the prenylated proteome", Charuta Palsuledesai, PhD, Postdoctoral Candidate (Wandinger-Ness & Bearer, hosts).
9:00 AM, CRF 204

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Thursday, OCTOBER 8

STMC Short Presentations. "Summer 2015 at a Pharmaceutical Company" by Prashant Dogra, UNM Cancer Center and "Studying EGFR signaling through modeling and single molecule imaging" by Emanuel Salazar Cavazos, UNM Pathology Department.
4:00-5:00 PM, CRF G25

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Friday, SEPTEMBER 25

CMBD Seminar: Pamela Bjorkman, PhD, Max Delbrück Professor of Biology and Investigator, HHMI, California Institute of Technology. "Architecture of antibody binding to virus". HIV/AIDS remains a threat to global public health because there is no effective vaccine. Following HIV infection, the human immune response is unable to clear the virus, partly because the virus rapidly mutates to evade antibodies. Antibodies generally neutralize viruses by bivalent binding to neighboring virion spikes. We propose that HIV's low spike density impedes bivalent antibody binding, minimizing avidity and potent neutralization, thus expanding the range of spike mutations permitting antibody evasion. HIV spike architecture prohibits intra-spike crosslinking by naturally-occurring antibodies, but we engineered high-avidity intra-spike binders with >100-fold average increased neutralization potencies, suggesting low spike density evolved to facilitate antibody evasion. These results shed light on dynamic spike conformations and are relevant to therapeutic interventions.
12:00 PM, Fitz Hall 203.

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Thursday, SEPTEMBER 24

The UNM Pathology Seminar Series: "Pathologic basis of central nervous system disorders", Elaine Bearer, MD, PhD, The Harvey Family Professor of Pathology, University of New Mexico. Download flier pdf icon
8:00 AM, Fitz Hall 303.

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Wednesday, SEPTEMBER 16

Technical workshop: Flowjo, with Flowjo technical rep Jack Panopoulos.
10:00 AM, CRF 204.

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Monday, AUGUST 31

Dissertation Defense: Yuna Guo (Mentor: Dr. Angela Wandinger-Ness). "R-ketorolac Targets Cdc42 and Rac1 and Alters Ovarian Cancer Cell Behaviors Critical for Invasion and Metastasis"
1:00 - 2:00 PM, Fitz Hall 303

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Friday, AUGUST 28

"Biophysics of axonal transport and implications for the brain", Elaine Bearer, MD, PhD, The Harvey Family Professor of Pathology, University of New Mexico.
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4:00 PM, Physics Colloquium: Dane Smith Hall Room 125. Coffee, bagels, and doughnuts at 3:40 PM.

Monday, AUGUST 17

Yi Wang, PhD, Carnegie Mellon University, postdoctoral candidate (D. Lidke, host). "Visualization and Photosensitization of ErbB Recpetors".
4:00 PM, CRF G25.

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Thursday, AUGUST 13

Sandrasegaram Gnanakaran, PhD, Staff Scientist, Los Alamos National Laboratory, "Systems level study of drug resistance".
4:00 PM, CRF G25.

Monday, AUGUST 10

Technical seminar: Amnis Imagestream. The Amnis Imagestream combines the quantitative analysis of flow cytometry with fluorescence imaging capability. If you are interested in finding out more about the capability of this cutting edge piece of equipment, please attend the seminar.
3:00-4:00 PM, Fitz Hall (BMSB) 309.

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Friday, JULY 31

Mark James Miller, Ph.D., Associate Professor, Internal Medicine, Infectious Diseases, Immunology Program, Molecular Microbiology and Microbial Pathogenesis Program, Washington University in St. Louis
12:00 PM, CRF G25

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Monday, JUNE 8

"Careers for Biomedical PHDs outside Academics" Karen Riley, PhD, Biology Instructor, Central New Mexico Community College (CNM)
11:00 AM - 12:00 PM, CRF 204

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Monday, JUNE 8

"Novel approaches to leukemia therapeutics: making lemons into lemonade," Monica Guzman, PhD, Assistant Professor, Pharmacology in Medicine, Weill Cornell Medical College. UNM Cancer Faculty candidate.
12:00-1:00 PM, UNM Cancer Center Auditorium

Monday, JUNE 8

"Real-time dynamics of B2 integrins and intercellular cues in leukocyte migration -lessons from imaging and photoactivation" Young-min Hyun, PhD Faculty candidate, Departmnet of Molecular Genetics and Microbiology.
3:00-4:00 PM, Fitz Hall Room 309

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Thursday, MAY 14

"Genetically encoded optical and biological materials" Jennifer S. Martinez, PhD, Scientist, Center for Integrated Nanotechnologies / Institute for Materials Science, Los Alamos National Laboratory
4:00 PM, CRF G25

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Tuesday, APRIL 21

"New Things with FAPs: Tailoring functions of dyes and proteins for imaging and manipulation", Marcel Bruchez, PhD, Associate Professor, Department of Chemistry, Carnegie Mellon University
4:00 PM, CRF G25

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Thursday, APRIL 9

"Bistability and stochastic activation of NF-κB, IRF3 and STAT shape cells responses to poly (I:C)," Tomasz Lipniacki, Head of Laboratory for Modeling in Biology & Medicine, Polish Academy of Sciences
4:00 PM, CRF G25

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Thursday, APRIL 2

UNM Cancer Center Presents: Translational Cancer Biology and Signaling (TCBS) Program Scientific Update
"Single molecule imaging and FRET microscopy reveal that enhanced dimerization drives oncogenic activity of EGFR NSCLC mutants" by Diane S. Lidke, PhD, Associate Professor, Pathology, UNM and "Sequential superresolution imaging of multiple targets using a single fluorophores" by Keith A. Lidke, PhD, Associate Professor, Physics & Astronomy, UNM
11:30 AM: Lunch, UNM Cancer Center Foyer, 12:00 PM: Presentations, UNM Cancer Center Auditorium

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Friday, MARCH 27

Cell and Molecular Basis of Disease (CMBD) seminar: "An Adaptive Proteostasis Landscape Sculpts Protein Structure and Function in Human Health and Disease", William E. Balch, PhD, Professor, Departments of Cell and Molecular Biology, and Chemical Physiology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
12:00 PM, Fitz (formerly BMSB) 303

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Thursday, MARCH 12

"Introducing Geometric Effects in Rule-Based Models of the Shrimp Allergen Tropomyosin" by Bruna Jacobson, PhD, Postdoctoral Fellow, Physics Astronomy Department and "Reflected beam light-sheet microscopy for whole-cell 3D super-resolution microscopy" by Marjolein Meddens, PhD, Postdoctoral Fellow, Pathology Department.
4:00-5:00 PM, CRF G25

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Friday, FEBRUARY 20

Dissertation defense, Kimberly Kanigel Winner, "Mathematical Models of Ovarian Cancer".
1:00 PM, Castetter 57.


Wednesday, FEBRUARY 18

Translational Informatics Workshop

"Drug, Target, Disease, Population: How Informatics can Impact Healthcare"

Sponsored by Illuminating the Druggable Genome Knowledge Management Center & Translational Informatics Division, Department of Internal Medicine, UNM
8:00 AM - 4:00 PM, Domenici Auditorium

Monday, FEBRUARY 16

BSGP Alternative careers seminar series

John Davis, PhD, Director, Investigative Toxicology, Drug Safety Research and Development, Pfizer

All welcome-predoctoral, postdoctoral, faculty, staff. ​For graduate students and postdocs interested in talking with her further after her seminar, please email Judy Cannon (jucannon@salud.unm.edu) to RSVP for lunch and discussion from 12:00 - 1:30 PM.​​​
11:00 AM - Noon, CRF 204

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Tuesday, JANUARY 20

DISSERTATION DEFENSE ANNOUNCEMENT: Stephanie Jerman. Title: "OFD1 and the Polycystins As Part of a Conserved Signaling Microdomain in Primary Cilia". Mentor: Angela Wandinger-Ness, Department of Pathology
1:30 PM, Domenici West 2112

2014

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Monday, DECEMBER 15

Comprehensive Exam: M. Frank Erasmus. "Tonic Signaling by the Pre-BCR Complex as a Survival Mechanism in Precursor-B Acute Lymphoblastic Leukemia". Mentor: Bridget Wilson, PhD, Department of Pathology.
9:30 AM, CRF 204

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Thursday, DECEMBER 11

"Active matter transport and jamming on disordered landscapes". Seminar by Cynthia J. Olson Reichhardt, Technical Staff Member, Los Alamos National Laboratory
4:00-5:00 PM, CRF G25

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Monday, DECEMBER 8

"Taking the industry route: Perspectives on a career in biopharma", Alissa Chackerian, PhD, Principal Scientist, Biologics-Discovery Merck Research Laboratories.
11:00 AM, CRF 204

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Friday, DECEMBER 5

"Defining the Dynamic Activation State and Regulation of the Cancer Kinome", Gary L. Johnson, PhD, Kenan Distinguished Professor and Chair, Department of Pharmacoloy, University of North Carolina School of Medicine​​.
8:00 AM (Breakfast and Coffee to be provided), Innovation Discovery & Training Complex, Room 2135

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Wednesday, DECEMBER 3

"Nature versus nurture? Investigating mechanisms of central nervous system infiltration in childhood acute lymphoblastic leukaemia", Dr. Chris Halsey, University of Glasgow​​.
12:00-1:00 PM, CRF 204 (Lunch provided)

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Thursday, NOVEMBER 13

"Molecular Mapping of the Human Vasculature by in Vivo Phage Display" by Renata Pasqualini, Ph.D., Chief, Division of Molecular Medicine, UNM Department of Internal Medicine and "Antibodies against specific IgER phosphorylation sites, and moving towards intracellular sensors" by Andrew Bradbury, M.B.B.S., Ph.D., Biosciences Division, Los Alamos National Laboratory.
4:00-5:00 PM, CRF G25

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Wednesday, NOVEMBER 12

Sheng Liu, PhD, is presenting to current and potential users of the STMC Super Resolution core facilities on Wednesday, November 12, 2014, beginning at 2:00 PM, in CRF 204. Liu's talk will feature the bright field stabilization and channel registration implemented in our TIRF microscope. The bright field stabilization approach uses the bright field images of the target cell, by calculating the cross correlations between the reference image and the current image, to stabilize the stage drift within 10 nm in XYZ. This stage stabilization method is integrated in a new Matlab class that is dedicated for collecting super-resolution data. The channel registration collects a matrix of bead images at a set of predefined grid points on each channel, and generates the transform matrix from the beads' coordinates localized by a 2D Gaussian fit on the bead images.
2:00 PM, CRF 204

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Friday, OCTOBER 31

This week's Physics &Astronomy Colloquium will be presented by Keith Lidke on the topic of "Fluorescence Nanoscopy". View for more information
4:00 PM, Room 125, Dane Smith Hall, UNM

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Monday, SEPTEMBER 29

Masters Thesis Defense: Mario Paz. "Novel Microfluidic Platform for Pulse Ligand Exposure". Mentor: Diane Lidke, PhD, Department of Pathology.
2:30 PM, CRF G25

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Friday, SEPTEMBER 12

CMBD seminar by Rytis Prekeris, PhD, Associate Professor, Cell and Developmental Biology, University of Colorado Anshutz Medical Campus

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Thursday, SEPTEMBER 11

"Mathematical modeling integrated with experiments and clinical trials to understand tumor heterogeneity, drug delivery and treatment outcome". Seminar by Vittorio Cristini, PhD, Professor, Department of Pathology
Download abstract pdf icon
4:00-5:00 PM, CRF G25

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Friday, SEPTEMBER 05

"Role of Membrane Domains in Health and Disease." A CMBD seminar by Anne Kenworthy, PhD. Dr. Kenworthy is from the Department of Cell and Developmental Biology, Vanderbilt University School of Medicine and is hosted by Dr. Jennifer Gillette from the STMC. Dr. Kenworthy utilizes sophisticated biophysical techniques to understand the role of membrane protein complexes such as lipid rafts and caveolae in health and disease. Her lab has a long-standing interest in mechanisms of diffusion and works with biomathematicians to develop widely accessible methods to calibrate, measure and quantify protein and lipid diffusion in living cells. The Kenworthy lab applies these approaches to study novel protein complexes involved in autophagy, Alzheimer's disease, host-pathogen interactions, and pulmonary arterial hypertension.
12:00-1:00 PM, BMSB 303 (now Reginald Herber Fitz Hall)

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Wednesday, AUGUST 20

CBME Seminar: Jeremy S. Edwards, Ph.D.. "Technology Innovation For Long Read DNA Sequencing".
4:00 PM, Centennial Engineering Center Auditorium (Room 1041), UNM.

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Monday, JULY 28

The J. Robert Oppenheimer Memorial Committee is pleased to announce that Dr. Harold Varmus will deliver the 44th Oppenheimer Memorial Lecture on July 28, 2014. The title of his lecture is: "The History and Future of Cancer Research."
7:30 PM, Smith Memorial Auditorium, 1300 Diamond Drive, Los Alamos, NM

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Monday, JULY 07

Guest seminar by Siddartha Das, University of Texas at El Paso. Title: "Cyst formation by Giardia: stories told by sphingolipids, transport vesicles and lipid rafts"
Download abstract pdf icon
4:00-5:00 PM, CRF G25

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Thursday, MAY 29

Seminar by Roberto Weigert, PhD, Chief, Intracellular Membrane Trafficking Unit, NIH-NIDCR Title: "Unraveling the Coordination among membrane trafficking, actin cytoskeleton, and cell metabolism in live animals by using intravital microscopy."
4:00-5:00 PM, CRF G25

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Friday, MAY 09

"Integrating single molecule techniques to investigate initiating steps in the FCeRI signaling pathway" by Samantha Schwartz (Lidke lab) and "CD82 regulates spatial and temporal dynamics of integrin-mediated adhesion" by Christina Termini (Gillette Lab)
3:30-5:00 PM, CRF G25

Tuesday, APRIL 29

Dissertation defense, Meghan Pryor (Edwards group)
Title: "Spatial Stochastic Modeling of the ErbB Receptor Family"
2:00-3:00 PM, CRF G25

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Monday, APRIL 14

Seminar by Santiago Schnell, Associate Professor of Molecular & Integrative Physiology and Computational Medicine, Univ. of Michigan
4:00-5:00 PM, CRF G25

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Friday, APRIL 04

STMC presentation by Keith Lidke on "Science and Capabilities of the STMC Superresolution Core"
4:00-5:00 PM, CRF G25

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Tuesday, MARCH 25

Representatives from the Open Microscopy Environment (OME) will be visiting the STMC to give a presentation on their OMERO image management software.
9:00 AM, CRF G25

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Wednesday, MARCH 12

UNM Biomedical Engineering Seminar. Aaron K. Neumann, Ph.D.: "Micro- and Nanoscale Spatial Organization of Fungal Ligands and C-type Lectins during Innate Immune Fungal Recognition"
4:00 PM, UNM Centennial Engineering Center Auditorium (Room 1041)

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Friday, MARCH 07 (Rescheduled from Feb. 07 due to weather)

STMC presentations by Matt Graus (Neumann lab) and Cedric Cleyrat (Wilson lab)
3:30-5:00 PM, CRF G25

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Monday, FEBRUARY 24

Guest speaker: Walter Kolch, Systems Biology Ireland & Conway Institute, University College Dublin, Ireland
"Protein networks regulated by compartmentalised Ras signalling"
Download bio pdf icon
Download abstract pdf icon
4:00-5:00 PM, CRF G25

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Friday, FEBRUARY 14

Guest speaker: Wolfgang Weninger, University of Sydney
3:30-4:30 PM, CRF G25

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Tuesday, JANUARY 28

"Human antibodies from display libraries". Andrew Bradbury, Ph.D., Staff Scientist, Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico and Adjunct Professor, Department of Chemical and Nuclear Engineering, UNM
11:30 AM - Lunch to be provided in UNM Cancer Center Admin Room 1048
12:00 PM - Lecture to begin in UNM Cancer Center Admin Room 1048

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Monday, JANUARY 27

Guest speaker: Tyler Reddy, Ph.D., Oxford University. He will present: "Biophysical characterization of full-scale influenza and dengue virions"
Download abstract pdf icon
Website: http://sbcb.bioch.ox.ac.uk/currentmembers/reddy.php
4:00-5:00 PM, CRF G25

2013

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Tuesday, DECEMBER 10

Webinar: "Advances in controlling cell environment during dynamic live cell imaging". Presenters: Kurt Thorn, Ph.D. and Andrew Ball, Ph.D.Register here
9:00 AM MST.

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Friday, DECEMBER 06

STMC presentations by Cesar Augusto (Gnanakaran group, LANL): "Molecular Mechanism of Interfacial Adsorption of Disordered Cytoplasmic Tail of Immune Receptors to Membranes" and Christopher Valley (D. Lidke lab, Pathology): "Single molecule analysis of EGFR dynamics and dimerization using single particle tracking, hyper spectral microscopy, and super-resolution imaging".
3:30-5:00 PM, CRF G25

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Friday, NOVEMBER 22

CETI's November Seminar speaker is Dr. Rustom Antia from the Department of Biology at Emory University. He will be presenting "Design principles for a robust immune system"
12:00 PM (lunch will begin at 11:30 AM), 107 Castetter Hall, UNM Main Campus

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Friday, NOVEMBER 22

Webinar: "Quantitative Assessment of Single-Cell RNA Sequencing Methods". STMC's Elaine Bearer suggests trainees might be interested in this 45-minute webinar featuring Dr. Stephen Quake, Stanford University. He will discuss his recent Nature Methods publication.
12:00-1:00 PM MST

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Wednesday, NOVEMBER 20

Live Videocast: NIH will be hosting a special lecture from Dr. Arieh Warshel on multiscale modeling of complex biological systems. Dr. Warshel along with Drs. Martin Karplus and Michael Levitt won this year's Nobel Prize in Chemistry for the development of computer-based methods to model complex systems.
1:00-2:00 PM ET, http://videocast.nih.gov/.

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Wednesday, NOVEMBER 13

CBME Seminar: "Materials inspired from biology: perspectives from artificial life". Martin M Hanczyc, Associate Professor, Institute of Physics, Chemistry and Pharmacy, University of Southern Denmark.
4:00 PM, UNM Centennial Engineering Center Auditorium

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Friday, NOVEMBER 01

STMC presentations by Jin Yang and Francois Asperti-Boursin (J. Cannon lab, MGM)
3:30-5:00 PM, CRF G25

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Monday, OCTOBER 14

UNM Cancer Center Director's Lectureship Series Presents: "Spatial Systems Biology of Cancer", Joe W. Gray, Ph.D., Gordon Moore Endowed Chair, Chair, Department of Biomedical Engineering, Director, Center for Spatial Systems Biomedicine, Associate Director for Translational Research, Knight Cancer Institute, Portland, OR.
11:30 AM - Lunch to be provided in the UNMCC Foyer
12:00 PM - Lecture to begin in the UNMCC Auditorium

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Friday, OCTOBER 04

STMC presentations by Jim Werner (LANL) and Farzim Farzam (K. Lidke lab, Physics)
3:30-5:00 PM, CRF G25

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Wednesday, OCTOBER 02

MathWorks seminar: Using MATLAB for Image Processing. This seminar will be particularly valuable for anyone intending to use MATLAB to process, analyze and visualize images. We will begin by showing you how to import, display and examine images in MATLAB. We will then step you through a series of examples designed to demonstrate how MATLAB can be used in a wide range of applications to explore ideas and automate your workflow. View the complete session description and register at: https://www.mathworks.com/UNM2013
9:00-11:30 AM, Student Union Building (SUB), Lobo A&B rooms (2nd floor)

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Friday, SEPTEMBER 20

"Diversity of Receptor Tyrosine Kinase Signaling Mechanisms". Mark A. Lemmon, Ph.D., George W. Raiziss Professor and Chair, Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine
12:00 PM, BMSB 203

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Friday, SEPTEMBER 20

"What Can Chemical Reaction Networks Compute?" David Soloveichik, Fellow, UCSF Center for Systems and Synthetic Biology
12:00-12:50 PM, Centennial Engineering Center 1041

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Friday, SEPTEMBER 13

Klaus Hahn, University of North Carolina (host D. Lidke)
12:00 PM, BMSB 203

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Friday, AUGUST 30

Physics and Astronomy Colloquium
Dr. Katja Lindenberg, University of California, San Diego. Abstract: The random motion of entities in crowded or disordered environments may be hindered by obstacles, traps, and dead ends. As a result, the motion may be subdiffusive. Reaction kinetics among subdiffusive species are highly "anomalous" in that they are very different from those described by the familiar laws of mass action involving only global concentrations c(t) as a function of time. It is in general not even possible to write equations involving only local concentrations c(x,t) as one does in reaction-diffusion problems. We discuss these issues in the context of the very simplest binary reactions such as the evanescence reaction A -> 0.
4:00 PM, Room 125, Dane Smith Hall

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Thursday, AUGUST 22

STMC Graduate Student Pat Cutler announces his Dissertation Defense. "Protein-Membrane Dynamics: New Perspectives in FceRI Signaling through Signal Particle Tracking"
2:00 PM, BMSB 303

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Thursday, JULY 25

Postdoctoral candidate Nicole Chapman will be presenting a seminar on her graduate work on regulation of TCR signaling. The title of her talk is: "The related kinases FAK and Pyk2 serve distinct functions in TCR signal transduction".
9:00 AM, BMSB 389

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Tuesday, MAY 28

STMC graduate student Kasra Manavi will speak on his work at the 9th Annual UNM Computer Science Symposium.
10:15 AM, Centennial Engineering lecture hall

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Monday, MAY 06

"Model-based analysis of promiscuity in the phosphotyrosine signaling network motif". Ed Stites, M.D., Ph.D., Washington University.
12:00 PM, CRF G25

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Monday, APRIL 15

"Cell signaling by receptor tyrosine kinases; from basic principles to cancer therapy". Joseph Schlessinger, PhD, William Prusoff Professor of Yale School of Medicine; Chairman, Department of Pharmacology; Yale School of Medicine
12:00 PM, UNM Cancer Center Auditorium

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Friday, MAY 03

"Regulation of Vascular Cell Adhesion". Dr. Mark Ginsberg, Distinguished Professor of Medicine, University of California San Diego
12:00 PM in BMSB 203

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Monday, MARCH 04

Consortium Seminar: "Single particle tracking to determine the role of Membrane Receptor Diffusion In Cell Signaling". Dr. Diane S. Lidke.
1:30 PM, P&A 190

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Wednesday, FEBRUARY 27

UNM Biomedical Engineering Seminar: "Mapping and Modeling Receptors on the Plasma Membrane Landscape". Bridget S. Wilson, Ph.D.
4:00 PM, Centennial Engineering Center Auditorium (Room 1041), University of New Mexico

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Monday, FEBRUARY 11

INCBN IGERT Seminar: "Fluorescence Nanoscopy". Keith Lidke.
2:30 PM, Center for High Technology Materials (CHTM) Room 101

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Friday, FEBRUARY 08

"Molecular Dynamics Simulations of Cell Signaling Proteins". "Gnana" Sandrasegaram Gnanakaran, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory.
2:00 PM, Cancer Research Facility, G25

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Monday, FEBRUARY 04

INCBN IGERT Seminar: "Biomolecular Site Dynamics". William S. Hlavacek, Scientist 3, Theoretical Division, Los Alamos National Laboratory.
2:30 PM, Center for High Technology Materials (CHTM) Room 101

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Wednesday, JANUARY 30

"Innovative imaging approaches for insight into B cell signaling". Facundo Batista, Head, Lymphocyte Interaction Group, London Research Institute.
12:00 PM, CRF G25

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Tuesday, JANUARY 15

"Spatiotemporal organization of lymphocyte signaling systems as a regulator of function". Christoph Wuelfing, Professor of Immunology, School of Cellular and Molecular Medicine, University of Bristol
3:30 PM, CRF G25

2012

Monday, NOVEMBER 19

INCBN IGERT Seminar Monday November 19, 2:30

"A Rule-Based Modeling Approach to Investigate the Impact of ErbB Receptor Dynamics on Signal Initiation and Propagation"
Speaker: Meghan McCabe
Chemical & Nuclear Engineering
Monday, November 19, 2012, 2:30 – 3:00 PM
Rm. #101 Center for High Technology Materials (CHTM)

Friday, NOVEMBER 16

"Global Optimization by Conformational Space Annealing and its Applications to Various Biological Systems"
Dr. Jooyoung Lee
Korea Institute for Advanced Study
4:00 PM, Dane Smith Hall, room 125

Dr. Jooyoung Lee is a guest of Dr. Keith Lidke.If you are interested in meeting with the guest and/or if have questions for Dr. Lidke, please call contact him via phone (277.0302) or email (klidke@unm.edu)

One of the fundamental goals of modern sciences is to understand the nature of life, and deciphering the protein structure and its working mechanism lies at the very heart of this agenda. Due to the tremendous success of many genome projects, the number of available protein sequences reached over 18 million as of 2012, but less than 1% of these protein structures are known. Reliable and accurate protein structure prediction using only the sequence information is greatly in demand, but it remains as an unsolved problem even after many years of efforts. We intend to establish a successful protein modeling method that is solely based on direct application of principles excluding human interference in modeling steps. This should be contrasted to the common conception in the field that human expertise accumulated by many years of protein modeling is the most important asset for accurate protein structure prediction.

In this talk we will discuss recent progresses of our efforts in protein structure prediction. It appears that our newly proposed method, which is based on the direct and rigorous optimization of relevant score functions, can provides significant improvement for 3D modeling of proteins in the category of High-Accuracy Template-Based Modeling. Applications of highly accurate protein 3D models to various biological systems will be discussed. We will also discuss the issue of protein function annotation utilizing recent advances of community detection method coupled with machine learning. Optimal Community structure was detected by maximization of modularity, and we demonstrate that achieving higher modularity partitioning of a network is crucial for extracting hidden information. Finally, we show that protein function information can be extracted more efficiently than the best methods available.

Friday, NOVEMBER 16

"Biofilms: another way of looking at bacteria"
Paul Webster, Ph.D.
Associate Scientist and Director, Ahmanson Advanced EM and Imaging Center
Cell Biology & Genetics/Otolaryngology, University of Southern California
Keck School of Medicine

Friday, November 16, 2012
BMSB 203, 12:30 PM

Friday, NOVEMBER 02

STMC Seminar
2:00 - 3:30 PM, CRF G25

Dr. Olga Pontes, Dept of Biology
Title: "Nuclear small RNA pathways guiding formation of Heterochromatin In Plants"

Dr. Jin Yang, Visiting Scholar, Pathology/STMC
Title: "Origins of concentration dependence of waiting times for single-molecule fluorescence binding"

Wednesday, OCTOBER 31

UNM Biomedical Engineering Seminar, October 31st, 2012
"Time-resolved three dimensional molecular tracking and nanocluster probes that fluoresce upon DNA hybridization"
James H. Werner, Ph.D.
Center for Integrated Nanotechnologies
Materials Physics and Applications Division
Los Alamos National Laboratory

Wednesday, October 31st, 2012
4:00 PM
Centennial Engineering Center Auditorium (Room 1041)
University of New Mexico

Abstract: Our lab has developed a method to follow the fast, 3D motion of individual fluorescently labeled proteins inside of live cells. Our method employs four overlapping confocal volume elements and active feedback once every 5 ms. This method has substantial advantages over three-dimensional molecular tracking methods based upon charge-coupled device cameras, including increased Z-tracking range (>10 microns), lower cellular photo damage, and the ability to perform time-resolved spectroscopy on the molecules being tracked. We have used these tracking methods to follow individual quantum dot (QD)-labeled IgE-FCεRI receptors both on and inside rat mast cells. We have also followed the 3D motion of individual dyes and individual green fluorescent proteins diffusing at ~1 micron^2/s rates. In addition to our 3D tracking efforts, our laboratory is also quite interested in the development of new fluorescent probes. In particular, we have developed a DNA-templated silver nano cluster probe that fluoresces brightly upon DNA hybridization and we have termed these probes NanoCluster Beacons (NCBs). We have demonstrated the use of an NCB for the sensitive detection of a nucleic acid sequence from avian flu and in the direct colorimetric detection of six disease-related single nucleotide polymorphisms (SNPs).

Wednesday, OCTOBER 17

"Protein Crystallography and Correlated Motions"
Michael Wall, PhD
Los Alamos National Laboratory
4:00 PM
Centennial Engineering Center Auditorium, Room 1041
University of New Mexico

Abstract: Crystallographers have produced hundreds of thousands of beautiful protein structure models. Unfortunately these models ignore the rich dynamics of real proteins. Electron density maps can provide evidence for the existence of alternative local configurations in a crystal, but do not constrain the way that transitions among these configurations are correlated across the whole protein structure. Fortunately we can say something about the correlations using diffuse X-ray scattering, which accounts for about half of the scattered X-rays in a typical crystallography experiment. As crystallographers face the limits of the information that can be extracted from Bragg peaks, diffuse scattering holds the potential to further improve protein crystal structures, to yield insight into functionally important motions, and to validate molecular dynamics simulations of proteins.

Friday, SEPTEMBER 21

"Modeling Proteins, Membranes, and Signal Transduction"
Seminar: Ravi Radhakrishnan, PhD
Associate Professor, Bioengineering & Chemical and Biomolecular Engineering, University of Pennsylvania
2:00 in CRF-G25

Abstract: In this talk, we will focus on applications of molecular and mesoscale simulation methodologies to the cellular transport process of endocytosis and exocytosis, i.e., active transport mechanisms characterized by vesicle nucleation, budding, and tabulation of the cell membrane orchestrated by protein-interaction networks. We will discuss theoretical and computational methodologies for quantitatively describing how cell-membrane topologies are actively mediated and manipulated by intracellular protein assemblies. We will describe the development and application of Monte Carlo methods and molecular dynamics methods for unified dynamics of curvature-inducing proteins, functionalized nano particles, and membranes. Our models provide mechanistic insight into "hidden" traffic rules in intracellular trafficking mechanisms.

Monday, AUGUST 20

"The Immunomics of Lymphocyte repertoires (a tasting menu)"
Guest speaker: Ramit Mehr, PhD
The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel
4:00 in CRF 204

Title: "The Immunomics of Lymphocyte repertoires (a tasting menu)"

Abstract: The immune system is a highly complex system, capable of cognitive tasks such as pathogen recognition, decision, learning and memory. This is a distributed system, in which the tasks are performed by an interacting network of specialized cells - primarily lymphocytes. Immune learning and memory are embedded in the dynamical states of the complete lymphocyte repertoire, and cannot be understood by studying the behavior of single cell types. This complexity, further increased by the non-linear behavior of each component, can only be elucidated by using theoretical tools to complement experimental and clinical studies. I shall review several examples of the use of such tools in immunological research, from modeling the NK cell immune synapse to lineage tree-based immunoglobulin gene informatics.

Wednesday, JUNE 20, 2012

"Mysteries of C-Type Lectin Domains in the Plasma Membrane of Dendritic Cells Explored By Super-Resolution Imaging and Nanoscale Measurements of Lateral Mobility"
Dr. Michelle S. Itano
Wednesday, June 20, 12:00 in CRF 204

Dr. Itano is a visiting scientist working in Dr. Aaron Neumann's research laboratory through June 22.

Abstract: DC-SIGN, a Ca2+-dependent C-type transmembrane lectin, is found assembled in microdomains on the plasma membranes of dendritic cells. These microdomains bind a large variety of pathogens and facilitate their uptake for subsequent antigen presentation. In these studies, DC-SIGN dynamics and distribution in microdomains have been explored with several fluorescence microscopy methods and compared with those for influenza hemagglutinin (HA), which is also found in plasma membrane microdomains. Fluorescence recovery after photobleaching (FRAP), line-scan fluorescence correlation spectroscopy and defined valency quantum dot single particle tracking measurements showed that full-length and cytoplasmically truncated DC-SIGN is essentially immobilized in microdomains, whereas HA is laterally mobile within and outside microdomains and exchanges between these two regions. By contrast, FRAP measurements indicated that inner leaflet lipids are able to move through DC-SIGN microdomains. Wide-field fluorescence imaging indicated that DC-SIGN microdomains may contain other C-type lectins and that the DC-SIGN cytoplasmic region is not required for microdomain formation. A super-resolution imaging technique, Blink Microscopy (Blink), was applied to further investigate the lateral distribution of DC- SIGN. Blink indicates that DC-SIGN, another C-type lectin (CD206), and HA are all localized in small (~80 nm in diameter) nanodomains. DC-SIGN and CD206 nanodomains are randomly distributed on the plasma membrane, whereas HA nanodomains cluster on length scales up to several microns. We estimate, as a lower limit, that DC-SIGN and HA nanodomains contain on average two tetramers or two trimers, respectively, while CD206 is often non-oligomerized. Two-color Blink determined that different C-type lectins rarely occupy the same nanodomain although they appear co-localized using widefield microscopy. Thus, a novel domain structure emerges in which elemental nanodomains, potentially capable of binding viruses, are organized in a random fashion; evidently, these nanodomains can be clustered into larger microdomains that act as receptor platforms for larger pathogens like yeasts. These results contribute significantly to a young field directed at elucidation of the complex intradomain structural features underlying function. (Supported by NIH GM-41402.)

Tuesday, JUNE 05, 2012

"TIRF based FRET Microscopy: New Methods for Imaging Molecular Complexes on the Cell Surface"
Jia Lin, postdoc candidate
9:30 AM in the Harvey Library (309 BMSB)

Abstract: Fluorescence Resonance Energy Transfer (FRET) microscopy measures the interaction between donor- and acceptor-labeled proteins in living cells. In widefield and confocal microscopy, the image is degraded by out-of-focus light. Total internal reflection Fluorescence (TIRF) microscopy can selectively excite molecules within about 150 nanometers of the glass-water interface, thereby eliminating out-of-focus fluorescence. However, interference fringing of the coherent laser illumination used in TIRF creates artifacts that prohibit quantitative imaging methods that require multiple laser illuminations such as FRET. Here we describe multicolor, depth-matched, 360-degree spinning TIRF illumination to enable quantitative, high-resolution FRET imaging of molecular complexes near the plasma membranes of living cells. In applying this method to cell biology, we have started to investigate the signal transduction of Fcγ receptor- mediated activation of macrophages using planar lipid bilayers presenting freely diffusing IgG molecules.

Friday, MAY 25, 2012

"A microfluidic platform for capture of circulating tumor cells from blood and downstream molecular analysis"
Kalyan Handique, Ph.D.
CEO, DeNovo Sciences, Michigan
9:00 AM, CRF 204

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 19strong><br>

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

Friday, MARCH 16

"Novel regulators of mast cell activity and number"
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

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)
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"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)
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"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 pdf icon
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-users.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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