Education

X-ray free electron lasers (XFELs) present unique capabilities to revolutionize structural biology and its ability to probe the biological world. As the NASA Apollo era captured a generation's interest in outer space, these unique capabilities have the potential to capture the imagination of students, teachers, and potential scientists interested in inner space; we will foster this effect through our education and diversity programs. The BioXFEL Center is committed to building a culturally and academically diverse, inclusive community of scholars. We aim to make STEM studies exciting and accessible for all students, postdoctoral fellows, faculty and staff.

The BioXFEL Science and Technology Center encompasses wide areas of scientific and technical expertise. We strive to reflect our communities and make opportunities available by embracing diversity in people as well as ideas. We aim to ensure the broadest representation of expertise and opportunity for education driving our science and building the scientific community for the future.

External Funding & Resources

To supplement our Diversity Programming, we have identified several useful resources run by our partner organizations that may be useful to you.

 

Opportunities

BioXFEL has partnered with the Institute for Broadening Participation (IBP), to both advertise our programs and provide additional resources to our members. IBP hosts a searchable database of internships, scholarships, and fellowships specifically for Underrepresented Minorities in STEM. Their resources library contains a range of professional development tips for students, as well as diversity resources and best practices for faculty and staff in STEM.

Funding

 

Pandemic Resources

BioXFEL COVID-19 ResourcesI'm sure all of you are tired of hearing how these are "unprecedented" or "challenging" times. We are all living through this together and are fully aware of the impact it is having on our daily lives, families, and communities.

Instead of reminding you of our hardships, we would like to offer some resources that may help. We have compiled below several resources that can help you get through this and come out on the other side as a better researcher, student, and mentor..

Read more...

COVID-19 Pandemic Response Initiatives

At the request of the National Science Foundation, BioXFEL will be collecting information on the impact of the current pandemic on our graduate students and postdocs. The Center will be requesting information on the impact on career progression, ability to conduct research, and professional development. Using this information, we will create new initiatives and make suggestions to NSF Leadership on best practices to remedy the situation by creating new support mechanisms.

Please fill in the survey below. If you have any additional information to provide that is not requested in the survey, please contact Bill Bauer.

Sample Preparation Guidelines

Important Information for the Participants of the Structural Biology with X-rays Workshop

 

BioSAXS Practical Sessions Information

General Information:

This BioSAXS part of the workshop will be focusing on the introduction to solution X-ray scattering as a method to answer questions in current structural biology research. In addition to the introductory lecture where you will learn the basics of the techniques as well as some of the analysis methods, we will also offer a remote data collection session for SAXS, during which you can measure your own sample (that you must have sent before to SSRL).  On the second day we will also offer a data analysis tutorial, where you can work on your own data (if you have sent samples or some standard protein data we will take during the data collection session)

Here is some information and guidelines we’d like you to follow if you are interested in the SAXS part in order to get you prepared and make these sessions during the workshop run more smoothly.

Laptop computers:

It is highly recommended that students bring their own laptop computer for the remote data collection and data analysis tutorial. Please also make sure that you have the appropriate rights on your machine that you can install software on it. Install the ATSAS suite (http://www.embl-hamburg.de/biosaxs/download.html) from the EMBL group in Hamburg onto your computer (it comes in a windows, mac and linux flavors). Try to see if you can run it (e.g. open primusqt, which is one of the programs in the suite), there won’t be enough time during the workshop to troubleshoot the installation.

For the remote access data collection we use the NX client (https://www.nomachine.com/), which is the same as the one you will use for the crystallography remote access. Please follow their guidelines for the installation and testing.

Also recommended is a program such as PyMol or UCSF Chimera to visualize structural models.

 

Measuring your own SAXS sample:

For those of you who intend to send a sample to SSRL to be measured during the remote session of the workshop please contact Thomas Weiss ( This email address is being protected from spambots. You need JavaScript enabled to view it. ) in order to coordinate the shipment. The samples should be at SSRL no later than Thu. Jan 23, 2020

  • let us know details about the size and composition of your sample (we will need that to reasonably group your measurements together) as well as a short text on the scientific merit and background.
  • please limit your number of samples to be less than four (not counting the dilutions); we cannot guarantee to be able to run more than that per participant during the workshop
  • if you need SEC-SAXS please specify clearly and let us know why you think you need that; for SEC-SAXS we can at most run 2 samples;If you prepare your own sample please follow the sample preparation and shipment guidelines below

Sample Shipment:

  • Unless your protein absolutely doesn’t like to be frozen, send your samples on dry ice. Alternatively you can send your samples also on wet ice using ice packs (but make sure that you mark the storage temperature clearly on the outside of the box, see also below).

    Address the package to:

     your name

    BL4-2, UPR Workshop

    c/o Dr. Thomas Weiss

    SSRL/SLAC Bldg 120

    2575 Sand Hill Rd.

    Menlo Park, CA 94025

    USA

    Again, please clearly mark on the outside of the box whether the samples need to be kept at -80C or at 4C after arrival at SSRL.

    Sample preparation guideline for solution x-ray scattering studies:

    Buffer solution: In solution scattering experiments, the signal arises from the electron density difference (contrast) between solute and solvent solution. One thus must perform successive measurements of the buffer solution alone (buffer) and the protein in the same buffer solution (sample). It is crucial to match the composition of the buffer to that of the sample within a small fraction of 1mM for each chemical component. The use of dialysis outer solution as the buffer solution is ideal, but not required as long as component concentrations can be matched. Alternatively, you can use the run-off buffer from the final size exclusion chromatography step.

    Buffer composition: most buffer solutions (pH 4-10) with or without salt at typical physiological concentrations should be adequate. If you have the choice between high salt and low salt buffer use the one with lower salt concentration, unless your protein is better soluble at the higher salt concentration. Using glycerol up to 5% is OK, but make sure you have the exact matching buffer for the background subtraction. Avoid detergents! Please bring at least several ml of buffer solution.

    Sample concentration: A series of concentrations typically between 0.5mg/mL and 10mg/ml (for instance 1-2-4-8 mg/mL), should be measured to evaluate inter-particle interaction behaviors. A rule of thumb for the high concentration is:

    mol.weight   x  max. concentration ≈100

    However if you sample aggregates before that send your protein in the highest concentration possible without forming detectable aggregates. Determine the concentration of your stock protein solution in advance for concentration scaling during data processing.

    Sample volume: Single set of measurements requires 30μl of a sample aliquot per dilution and takes approximately 3 minutes. A minimum of 3 dilutions per sample should be measured. We will spin down your sample before pipetting the dilution series (unless you tell us explicitly not to) and will pipette off the top so it would be good to have a bit of excess sample if possible.

    Buffer solution: In solution scattering experiments, the signal arises from the electron density difference (contrast) between solute and solvent solution. One thus must perform successive measurements of the buffer solution alone (buffer) and the protein in the same buffer solution (sample). It is crucial to match the composition of the buffer to that of the sample within a small fraction of 1mM for each chemical component. The use of dialysis outer solution as the buffer solution is ideal, but not required as long as component concentrations can be matched. Alternatively, you can use the run-off buffer from the final size exclusion chromatography step.

    Buffer composition: most buffer solutions (pH 4-10) with or without salt at typical physiological concentrations should be adequate. If you have the choice between high salt and low salt buffer use the one with lower salt concentration, unless your protein is better soluble at the higher salt concentration. Using glycerol up to 5% is OK, but make sure you have the exact matching buffer for the background subtraction. Avoid detergents! Please bring at least several ml of buffer solution.

    Optional items: Sulfur-reducing agents such as DTT, TCEP, and 2-mercaptoethanol often protect proteins from excessive radiation damage. If your protein tolerates, use one of them at 1-5mM. The use of glycerol or lower/higher salt concentration may help maintain sample monodispersity.

     

    Crystallography Sample Preparation and General Guidelines

    For those of you planning on sending in crystals to SSRL, please refer to the instructions found HERE. This provides information on acceptable pin types and best practices to optimize the process.

    Our final deadline for receiving samples at SSRL is January 17th. Please be sure that they arrive before this date and that SSRL is notified of the shipment