> Workshops

 

Next Workshops:


May 4-8, 2020  at the National Institutes of Health, Bethesda

By the Foundation for Advanced Education in the Sciences.  For more detailed information see https://faes.org/events/biophysical-methods-boot-camp-2020, or contact Peter Schuck (schuckp@mail.nih.gov)

 


Workshop History:

The workshops have been held both at the National Institutes of Health in Bethesda and in many international locations, such as the Institut de Biologie Structurale, Grenoble, France, the University College London, U.K., the École Polytechnique Fédérale de Lausanne, Switzerland, the Uppsala Unversity, Sweden, the Medical School Hannover, Germany, and more recently at the University of Oxford, U.K., the Centro Investigaciones Biologicas in Madrid, Spain, and the Yokohama City University in Yokohama, Japan.  Since 2004, more than 400 scientists from academia and industry of more than 20 countries have participated in the workshops, which has advanced numerous research projects and resulted in hundreds of publications.
 
 
 

Workshops for the hydrodynamic and thermodynamic analysis of biological macromolecules and their interactions with SEDFIT and SEDPHAT are being held 2 – 3 times a year, at NIH as part of the bootcamp series of the Foundation for Advanced Education in Sciences (FAES), or hosted in other academic institutions. 

The workshops are typically for one week, and consist of lectures on the biophyiscal theory and applications of several biophysical techniques (analytical ultracentrifugation, isothermal titration calorimetry, surface plasmon resonance biosensing, fluorescence spectroscopy), practical exercises in the lab, practical computational analysis exercises, and individual data analysis sessions. 

Attendance is limited, and registration is required.

 

Topics:

The list of topics will depend on the focus and length of the workshop, usually including the following:

Overview of Biophysical Techniques
  • Introductions of AUC, ITC, SPR, static and dyanmic light scsattering,  small angle scattering, fluorescence, and other

Experimental

  • Experiment design in AUC: choice of concentrations, buffers, optical systems; sample volumes, noise types, meniscus considerations
  • Conducting the AUC experiment: assembly of ultracentrifugal cells, adjustment of optics, operating the XLA/I, using the Aviv fluroescence detector
  • Operating the ITC and experimental design
  • Operating the DLS and experimental design

Theory and Practical Data Analysis

  • General aspects of non-linear regression and statistical error analysis
  • Global analysis concepts with SEDPHAT
  • Overview of data organization in SEDPHAT, and exporting data from SEDFIT to SEDPHAT
  • Overview of sedimentation velocity analysis with SEDFIT
  • Discrete species analysis by direct boundary modeling
  • Sedimentation coefficient and molar mass distributions
  • Interpretation of the goodness of fit, frictional ratio, and statistical analysis
  • Enhancing sensitivity and resolution by incorporating prior knowledge in c(s) with new Bayesian approach
  • Example:  The detection of trace oligomeric components
  • Size-and-Shape distributions c(s,M) and c(s,f)
  • scale-free general sedimentation coefficient distribution c(s,*)
  • Sedimentation equilibrium analysis:  global analysis of multi-wavelength data
  • Sedimentation equilibrium analysis with soft mass conservation models
  • Hybrid discrete/continuous sedimentation coefficient distribution analysis
  • Analysis of self-associating systems by c(s), isotherms, and direct boundary modeling
  • Analysis of hetero-associating systems by sedimentation velocity
  • The effective particle explorer
  • Global modeling of the reaction boundary with Lamm equation solutions
  • Multi-signal sedimentation velocity analysis for heterogeneous interactions
  • Hydrodynamic interactions
  • Dynamic light scattering analysis in SEDFIT
  • ITC analysis for single and multiple titrations
  • ITC analysis of ternary interactions
  • global ITC analysis for linked binding (protonation, temperature, ions)
  • interpreting ITC results in framework of structural thermodynamics
  • SPR analysis in EVILFIT: continuous distributions of rate and affinity constants
  • General isotherm analysis with SEDPHAT
  • Spectroscopy data analysis: fluorescence quenching, circular dichroism, and others
  • Fluorescence anisotropy isotherm analysis

 

Format:  

For a full length NIH workshop, typically, the first workshop day will have brief introductory lectures for the different methodologies.  The practical aspects will be covered in a mixture of hands-on exercises and demonstrations.  This will take place largely in our laboratories, alternating with review and discussion of experimental strategies in the seminar room.  The following part of the workshop will be devoted to the practical data analysis and take place in a classroom.  The goal is to ensure through hands-on training that the participants become familiar with the details of the use of the software, and confident with each type of data analysis.  We will have a lecture series in the morning and early afternoon, to introduce and recapitulate the theoretical background as well as the concepts for their implementation in the software, mixed with practical exercises on examples, where each participant will conduct data analyses on his/her laptop concurrent with the step-by-step demonstration projected on the large screen.

From mid afternoon, the participants are expected to give short presentations on a topic of their interest.  This is very informal.  This can be, for example, a presentation of the biological background of a system of interacting proteins for which sedimentation analysis may be applied in the future; a presentation of an existing application of analytical ultracentrifugation; an introduction to another biophysical technique for studying macromolecules; the presentation of an open question regarding ultracentrifugation technique; the discussion of preliminary data; or simply the introduction of the speaker and her/his interests.  The purpose of this section is to learn about areas of application and to stimulate the discussion.  In the past, this section has become a favorite for most participants, since it allows to get to know each other's interests, and as a group to take advantage of unique expertise of each of the participants.    

 

 

 

 

Isothermal Titration Calorimetry Bootcamp
This bootcamp usually spans 2 - 3 days, and consist of hands-on lab, experimental design, and data analysis sessions for ITC, alternating with lectures on principles and applications, with opportunity for individual data analysis sessions. 
Attendance is limited, and registration is required.
 
Topics:
The list of topics will depend on the focus and length of the workshop, usually including the following:
 
Experimental
  • Experimental planning in ITC:  choice of concentrations, buffers, and desgin of experimental series for global analysis
  • Predicting information content of the experiments with the SEDPHAT simulation tool
  • Conducting the experiment: lab session on filling the cells, equilibration, instrument cleaning, control experiments

 

Theory and Practical Data Analysis
  • Principles of ITC and related biophysical techniques
  • Data organization and data import in SEDPHAT
  • High-precision integration of thermograms with NITPIC
  • Accounting for incompetent fractions and concentration errors
  • Global analysis of ITC data in SEDPHAT
  • Multi-site binding models
  • Ternary interactions, competitive and cooperative binding, and displacement assays
  • Linked binding for temperature dependence, pH dependence, and/or co-solute dependence
  • Global multi-method analysis
  • Background on non-linear regression and statistical error analysis

  

 
Format:  
The goal is to ensure through hands-on training that the participants become familiar with the details of ITC.  Each participant will conduct data analyses on his/her laptop concurrent with the step-by-step demonstration projected on the large screen.
  
 

 

 



 

 

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 verifying the sedfit and sedphat installation
 FAES