Fitzkee Lab
Fitzkee Lab
  • Видео 29
  • Просмотров 21 432
Grad Ambassador: Radha Somarathne
A recent video produced by the MSU TV Center featuring one of our recent PhD graduate students and Fitzkee Lab alum, Dr. Radha Somarathne. Congratulations on your accomplishments, Radha!
Просмотров: 317

Видео

The MSU NMR Facility: Welcome and Overview
Просмотров 185Год назад
This video introduces MSU General Chemistry Lab students to the NMR instrumentation and capabilities in the Department of Chemistry.
How to Make Sine Waves in Powerpoint
Просмотров 4,2 тыс.Год назад
Sometimes doing something the right way means finding the right tool. In this quick video, we look at how you can make clean sine or cosine waves (or any other function) for your presentations or illustrations.
Adding an NCBI RSS Feed to Feedly
Просмотров 160Год назад
This video, provided by Feedly tech support, shows how to add the NCBI search as an RSS feed in Feedly. The key is to paste, then to press enter or return (do not click the search result that appears).
Helium Recovery and Recycling on a Budget, Part 1: Overview and General Plan
Просмотров 217Год назад
We’re starting the process of upgrading the MSU NMR Facility with a helium recovery system and new 800 MHz NMR instrument. Join us as we learn the basics and work to install a low cost (bagless) helium system over the next year! In this video, we introduce the planned system and outline some of the constraints in our mid-sized NMR facility. We’ll cover the basic calculations and considerations ...
NMR Basics, Part 3: Managing Assignments in Your HSQC with Sparky and POKY
Просмотров 451Год назад
In this final video, we take our processed NMR spectrum and open it in two visualization tools, NMRFAM-Sparky, and Sparky’s successor POKY. We look at how to change contouring and examine how you might interactively copy peak assignments in a spectrum. Here are the data files we will use in this video: Unprocessed NMR Spectrum: fitzkee.chemistry.msstate.edu/sites/default/files/youtube/k19g_hsqc...
NMR Basics, Part 2: Processing Your HSQC in Linux with NMRPipe
Просмотров 463Год назад
In this video, we discuss how NMRPipe processes NMR spectra. We look at the file format for a standard NMRPipe processing script, and we examine the basic parts of the script and talk about what they do. Finally, we discuss why it may be beneficial to look at a spectrum that is only processed in one dimension. Here are the data files we will use in this video: Unprocessed NMR Spectrum: fitzkee....
NMR Basics, Part 1: Transferring Your Bruker HSQC to Your Workstation and Preparing for Processing
Просмотров 614Год назад
In this video, we look at how you can transfer your newly-collected NMR data from the NMR PC to your Linux workstation. Then we look at the basic tools for converting a standard HSQC into a file that can be read and processed by NMRPipe. Here are the data files we will use in this video: Unprocessed NMR Spectrum: fitzkee.chemistry.msstate.edu/sites/default/files/youtube/k19g_hsqc.zip Processing...
Literature Databases and Using EndNote (Session #13, Biochemistry Boot Camp 2021)
Просмотров 523 года назад
All science is built on the foundation of previous experiments, and the results of these experiments can be found in scientific publications. In this session, Dr. Joanna Xu from Mississippi State University, a postdoc in the Fitzkee Lab, explains what the scientific literature is, and she suggests effective ways to search for scientific papers. Finally, she demonstrates how EndNote software can...
The PDB and Molecular Visualization (Session #9, Biochemistry Boot Camp 2021)
Просмотров 1273 года назад
How can we find out what a protein’s structure is, and once we have the coordinates, how do we display them? Is molecular visualization good for anything more than making pretty pictures? Dr. Nick Fitzkee from Mississippi State University takes a closer look at the Protein Data Bank (PDB) and describes how you can find and identify high quality structures. He then introduces the PyMOL molecular...
Getting Started with Python (Session #12, Biochemistry Boot Camp 2021)
Просмотров 3543 года назад
Learning how to program a computer is one of the most useful skills any scientist can develop. Here, Dr. Nick Fitzkee from Mississippi State University introduces the Python programming language. This video is designed to help students with little programming experience install Python and understand how programs can be developed in this powerful language. Dr. Fitzkee does not cover the specific...
Bioinformatics, Sequence Alignment, and Homology (Session #11, Biochemistry Boot Camp 2021)
Просмотров 1,6 тыс.3 года назад
Databases of biomolecular sequences allow for the identification and comparison of protein and nucleic acids across many different organisms. In this video, Dr. Nick Fitzkee from Mississippi State University discusses how sequences can be compared, and how rapid comparison of sequences allows user to search vast databases of genetic information. Finally, he discusses how this sequence compariso...
Laboratory Notebooks (Session #10, Biochemistry Boot Camp 2021)
Просмотров 683 года назад
Maintaining an accurate laboratory notebook is the foundation to reproducible science. In this session, Dhanush Amarasekara from Mississippi State University, a graduate student in the Fitzkee Lab, talks about the basics of laboratory notebooks. Then, he moves on to more advanced topics, including digital archival, and what to do when your data won’t fit in a paper notebook. Session #10 of Bioc...
Calculating DNA Properties (Session #8, Biochemistry Boot Camp 2021)
Просмотров 1133 года назад
Dr. Chris Johnson from Mississippi State University returns to describe the online tools that can be used to make predictions about nucleic acids. He outlines websites that can predict the extinction coefficient for DNA and RNA, and he examines calculations of the melting temperature. Finally, he describes how these tools can be used to perform PCR and site-directed mutagenesis. Session #8 of B...
Nucleic Acids and Molecular Biology (Session #7, Biochemistry Boot Camp 2021)
Просмотров 713 года назад
In this session, Dr. Chris Johnson from Mississippi State University reviews the fundamentals of DNA structure and why nucleic acids are important in the study of biochemistry. He also reviews the molecular biology of bacterial protein expression systems, which many students use in their summer research projects. Session #7 of Biochemistry Boot Camp 2021 (June 7-10). Download the lecture slides...
Publication Quality Graphics (Session #6, Biochemistry Boot Camp 2021)
Просмотров 763 года назад
Publication Quality Graphics (Session #6, Biochemistry Boot Camp 2021)
Model Fitting Using Excel and Gnuplot (Session #4, Biochemistry Boot Camp 2021)
Просмотров 2323 года назад
Model Fitting Using Excel and Gnuplot (Session #4, Biochemistry Boot Camp 2021)
Introduction to UNIX/Linux (Session #3, Biochemistry Boot Camp 2021)
Просмотров 1213 года назад
Introduction to UNIX/Linux (Session #3, Biochemistry Boot Camp 2021)
Digitally Assessing Protein Properties (Session #2, Biochemistry Boot Camp 2021)
Просмотров 1173 года назад
Digitally Assessing Protein Properties (Session #2, Biochemistry Boot Camp 2021)
Protein Structure (Session #1, Biochemistry Boot Camp 2021)
Просмотров 4613 года назад
Protein Structure (Session #1, Biochemistry Boot Camp 2021)
How to Merge and Touch-Up Multiple Graphs Using Adobe Illustrator
Просмотров 1 тыс.4 года назад
How to Merge and Touch-Up Multiple Graphs Using Adobe Illustrator
How to clean and prepare a super loop for use in an AKTA FPLC system
Просмотров 8 тыс.4 года назад
How to clean and prepare a super loop for use in an AKTA FPLC system
MSU Chemistry Awards Banquet 2020 - Phi Lambda Upsilon Inductees
Просмотров 474 года назад
MSU Chemistry Awards Banquet 2020 - Phi Lambda Upsilon Inductees
MSU Chemistry Awards Banquet 2020 - Thermo and Kinetics Award
Просмотров 534 года назад
MSU Chemistry Awards Banquet 2020 - Thermo and Kinetics Award
MSU Chemistry Awards Banquet 2020 - Phi Beta Kappa Award
Просмотров 704 года назад
MSU Chemistry Awards Banquet 2020 - Phi Beta Kappa Award
How to make NMR strip plots using Sparky and Adobe Illustrator
Просмотров 1,4 тыс.4 года назад
How to make NMR strip plots using Sparky and Adobe Illustrator
Biochemistry Boot Camp 2018: Session #3 - Linux
Просмотров 916 лет назад
Biochemistry Boot Camp 2018: Session #3 - Linux
Biochemistry Boot Camp 2018: Session #2 - Protein Properties
Просмотров 966 лет назад
Biochemistry Boot Camp 2018: Session #2 - Protein Properties
Biochemistry Boot Camp 2018: Session #1 - Protein Structure
Просмотров 7986 лет назад
Biochemistry Boot Camp 2018: Session #1 - Protein Structure

Комментарии

  • @tomgriffin4331
    @tomgriffin4331 23 дня назад

    Wow, Fitzkee Lab, that is terrific! Huge help. Thank you so much for the foundational idea and the cool variants. Great job!

  • @AerialOwens-uv5iq
    @AerialOwens-uv5iq 4 месяца назад

    Great video! Thanks for stepping through each of the processes in Parts 1 and 2. I generally use ccpn but the Sparky info is helpful too

  • @kannanp2000
    @kannanp2000 4 месяца назад

    Thank you very much. I never thought of doing this through excel. This is very helpful.

  • @GMAdamFahmy24
    @GMAdamFahmy24 5 месяцев назад

    Thank you very much, man! I have a physics project due next week and I was really struggling with myself. You're a live saver :D

  • @ashishnandeshwar
    @ashishnandeshwar 7 месяцев назад

    This was really helpful 😮

  • @LeeGroupatCUDenver
    @LeeGroupatCUDenver Год назад

    Thanks, Nick. I can explain about some hiccups in the video. 1. UCSF/NMRFAM-SPARKY has some issues in the relative path resolution. Relative paths saved by them are incorrect if they are complicated sometimes. Latest POKY shouldn't have a problem. 2. Read peak list (rp) is an extension and not a built-in. It is in the Ext. -> Peak menu. It is the same both POKY and SPARKY. 3. Select visible labels (Lv) and peaks (pV) are in the latest POKY. Woonghee

  • @ericyoung7224
    @ericyoung7224 Год назад

    Thanks for this!

  • @emdadsami
    @emdadsami 2 года назад

    Thank you Prof. Fitzkee for this lecture- Emdad

  • @Prince-oe6yv
    @Prince-oe6yv 2 года назад

    Thank you for this demonstration, exactly what I was looking for :)

  • @_ADHK293A_
    @_ADHK293A_ 2 года назад

    thank you for this contet

  • @odin-fr9et
    @odin-fr9et 2 года назад

    I remember learning this when i was in school. Something got me thinking about this today,thats why im hear. Thank for the video.

  • @mahmudulhasan14
    @mahmudulhasan14 3 года назад

    Worth watching. Interesting chemistry. Thank you for this informative video.

  • @hariprakash4402
    @hariprakash4402 3 года назад

    Please share more videos on Akta sample loading using Pump p950

    • @FitzkeeLab
      @FitzkeeLab 3 года назад

      Hi Hari! That's actually something I don't have a lot of expertise on. My postdoc has used the sample pump in one of his former labs, but it was always one of the luxuries that we never purchased in the labs I was trained in. As a result, I built up some mighty strong forearms during my postdoc years!

  • @shadrums
    @shadrums 3 года назад

    What's the process for putting protein sample into the loop next?

    • @FitzkeeLab
      @FitzkeeLab 3 года назад

      The standard way is to load a disposable syringe with your sample (anywhere from 1-50 mL), attach a 0.45 um syringe filter to the end, dispense enough of your sample so that it fills the syringe filter and that there are no bubbles at the tip, and then simply inject your sample into the sample port in the injection valve. The default state for the injection valve, if no program is running in Unicorn, is the "load" state, which means sample injected into the load port will go into the loop as you inject. I never take this for granted, and I'm always looking at the super loop as I inject to make sure the stopper is moving up as I add my sample. I also look at the waste line from the injection valve: as I inject sample into the loop, buffer is displaced from the top of the loop, and that buffer gets directed to waste. Once my sample is injected, I can either start a program or manually run the sample. Most of my trainees do nickel and ion exchange columns manually these days, and we only use programs for our gel filtration columns, but either way, once the sample is in the loop, you can do what like from there. A final note: sometimes using the 0.45 um syringe filter makes it really hard to inject your sample: You're ultimately trying to shoot typically 25-50 mL of viscous solution through a tiny channel carved in the injection valve (not to mention the PEEK tubing). Even without the filter, injecting it carefully without breaking the luer lock fitting can require a lot of upper body strength and control. I always tell my students to take their time and take a break if their arms get tired. It's not a race. However, if the syringe filter is making things too difficult, a hard spin in the centrifuge at 20-40,000 x g for 30 minutes is often enough to get most of the large insoluble material out of your sample, and if you do this step you can usually eliminate the filter. Hope that helps!

    • @shadrums
      @shadrums 3 года назад

      @@FitzkeeLab that was very helpful, thank you!!

  • @dxg1396
    @dxg1396 4 года назад

    Thank you so much! I've been trying to do this for a while now.

  • @LeeGroupatCUDenver
    @LeeGroupatCUDenver 5 лет назад

    Nice. I will make an extension for a user to adjust user settings when I have some time to work on.

    • @LeeGroupatCUDenver
      @LeeGroupatCUDenver 5 лет назад

      ... and it is here: ruclips.net/video/An73Bt01-e0/видео.html 44:13 In the new GUI tool ("fP"), you can set to false for all strips. Then, leave the one that you want to have tick marks and set to true..