[Demelerlab] phage project

[Borries Demeler]

Hi Phil,
this looks great, exactly what I had in mind. I am copying my group to see
if anyone is interested in working on this project.
Since this will be a multi-wavelength project, it would be very helpful to
get some proof-of-concept data from your samples first to make sure they
have the correct extinction ratios in order to be resolvable by
multi-wavelength.

Can you or your student please create a LIMS account in our server:

To request an account, please visit:
https://uslims.uleth.ca/uslims3_AUCCANADA/newaccount.php
You will be sent a temporary password, and after logging into your account,
you can change it with the "Change my Info" button.
After logging in, please also submit a project request ("Projects" button
on the left) and the following supporting files:

1. Absorbance spectra of the protein capsid
2. absorbance spectra of the DNA
3. absorbance spectra of the bleomycin solution.
4. absorbance spectra of the buffer
5. absorbance spectra of the samples you plan to send

PLEASE FOLLOW THESE IMPORTANT INSTRUCTIONS:

* all samples should be dialyzed/purified/dissolved in the *SAME* buffer
* the absorbance spectra should be from 240-300 nm and should be uploaded
in CSV format (ascii spreadsheet, comma separated values)
* the absorbance spectra should not exceed 1.0 OD in this range - dilute
them in the same buffer
* all samples should be available in a concentration that absorbs at least
1.0 OD in this wavelength range
* the volume needs to be sufficient so we can do both sed. velocity and
CsCl analytical buoyant density equilibrium (ABDE) experiments.  ABDE
experiments require significantly less signal since all signal will get
concentrated in a narrow peak.

We can have a zoom call to go over the spectral data you have to determine
if the experiment is suitable. I was looking for a bleomycin UV spectral
profile in the paper you provided, but couldn't find one. This is the first
crucial information we need to make sure this has a chance of working.

Thanks so much, -Borries


On Mon, Sep 25, 2023 at 3:03 PM Serwer, Philip <SERWER at uthscsa.edu> wrote:

> To continue, we had a lab meeting today and discussed the AUC. The plan is
> the following, if OK with you. We have a preparation of bleomycin-loaded
> phage T4 and another is being made in larger amount. The student doing this
> is Meagan Weaver-Rosen.
>
>
>
> The plan for the first AUC is to send our current preparation of
> bleomycin-loaded T4, along with unloaded T4 and bleomycin. We will also
> burst some T4 so that you have the capsid without DNA and the DNA without
> capsid together in one specimen. These two will separate during AUC. So,
> you can calibrate the multi-wavelength technique with purified versions of
> the three components: protein capsid, DNA and bleomycin.
>
>
>
> Hopefully, we will learn enough so that more detailed AUC can be done in
> the future when Meagan tests, for example, the amount of bleomycin loaded
> vs. temperature, time, etc.
>
>
>
> What do you think?
>
>
>
> Phil
>
>
>
> I have attached the key precursor manuscript.
>
>
>
> *From: *Borries Demeler <demeler at gmail.com>
> *Date: *Saturday, September 16, 2023 at 4:11 PM
> *To: *Philip Serwer <SERWER at uthscsa.edu>
> *Subject: *Re: phage project
>
>
>
> **EXTERNAL EMAIL**
>
>
>
> OK, great, let me know if you ever want to have a zoom meeting with
> everyone in case there are questions that are best answered by myself.
>
>
>
> Regards, -Borries
>
>
>
>
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