Synthetic biology in Rhodobacter: what a great fun

[BraveScience]

Hi,

Recently I started being interested in purple bacteria. More specifically I found Rhodobacter spheroides a very interesting organism.
It has all the gigs as a metabolic engineer you'd like to have from your chassis: heterotrophism, chemoautotrophism and photoheterotrophism.
I work with cyanobacteria for living but these purple beauties got my full attention.

It lives in waste water, loves all sugars (xylose from biomass isn't gonna be a problem, if it is we can fix it easily) and can live off the most incredible substrates, from methanol, H2 to poop.

Most importantly it's very pretty with all those red colors.

As I am looking into potential synthetic biological application, and metabolism rewiring and modelling, I was wondering if anybody has work before with such beautiful organism.

Find it interesting or have any heads up where to look? Please, drop me a line.

Best,
Fede

[Katherine Gordon]

Rewiring metabolism. Brilliant!

Hello Fede,
I studied biochemistry in. College in the late 90,s. Mitochondria were and still are my interest . You mention rewiring metabolism...How would you go about this trick? I would greatly be interested in your thoughts. A symbiotic relationship between these bacterial meto bolic engineers and our somatic cells is possibly the most remarkable thing Ive ever heard.
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[Katherine Gordon]

Please contact me directly at kthrn...@gmail.com my name is Kate.

[Brian Degger]

What are you interested in Kate?

It's somewhat nice to keep the conversation open on this diybio forum. Especially in the start. 

I can understand that you might have something to offer on the subject. And we(I use the royal we, I speak for myself and a few friends on DIYBio that I know well) would all love to hear it. We are interested in everything, and debating and finding out more. We are semi-dogmatic when it comes to self-gm in a kitchen(against), and (against) anything about using biology for evil, or letting people do damage by bio-error-ism after they have contacted the group. 

Also.. you give your personal email out to 4406+ people. I would be fine with that, because other people are always publishing my email to others and I want people to look at my public Google+ profile. You might not be so happy about that. 

Cheers,

Brian

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Brian Degger

twitter: @drbrian

http://makerspace.org.uk

http://transitlab.org

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[Dennis Oleksyuk]

Here is a paper from 2014 which claims that chemical or electroporative transformation does not work in Rhodobacter. They only where able to do it using conjugative transformation.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0086830 -  Search for Cloning of Rhodobacter AqpZ.

If you decide to follow the conjugation path, at least in USA, using e.coli capable of horizontal gene transfer requires you to follow the NIH Guidelines. Other people in this forum, who are more familiar with the topic, could better explain what it means.

http://osp.od.nih.gov/sites/default/files/NIH_Guidelines.html - Search for conjugat

Transformation of Rhodobacter in DIYBio setup is probably an interesting project by itself. Please, share you results if you get somewhere.

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[Katherine Gordon]

Thank you for sheparding. Having already given out my email to those numbers, perhaps more discretion is warranted, I am truly interested but you are correct in sensing a niavete about my communication style. I would like to address you personally due to fear of sounding undisciplined or lacking in knowledge to so many others. I am not doing anything DIY in a home lab, nor am I a bioterrorist, just a gal with an Interest in longevity and improved health as well as progressive adaptation of the human genome. All of this in theory only since I am well aware of ethical and pragmatic constraints on germ line manipulation. I am a sci-fi writer.

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[Brian Degger]

Katherine,
A lot of us are interested in longevity(or aging well) ....so ask some questions.

One of the aspects of aging seems to be related to mitochondria and the goldilox zone of free radical concentration. ..not to little not to much.

Most of us have seen Aubrey Grey talk about his project SENS that attempts to fix cells faster than they get damaged.

So ask a question. What do you want to know?

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[Mega [Andreas Stuermer]]

As for the transformation, you can always try carbon whiskers or glass beads. They transform litterally anything. Bacteria, Yeast, Algae, Mammalian cells, fungi, Plants. Best to use with PEG (both DNA and membrane bear a negative charge, PEG is positive).

Make sure not to inhale them though, they are like asbestos and may give you cancer.

[Brian Degger]

Sorry about the (off topic nes of my last few posts)

On 17 Nov 2015 10:52, "Mega [Andreas Stuermer]" <masters...@gmail.com> wrote:

As for the transformation, you can always try carbon whiskers or glass beads. They transform litterally anything. Bacteria, Yeast, Algae, Mammalian cells, fungi, Plants. Best to use with PEG (both DNA and membrane bear a negative charge, PEG is positive).

Make sure not to inhale them though, they are like asbestos and may give you cancer.

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[BraveScience]

Sorry for the late reply, got busy in the lab.

@Kate Thanks for the interest, as Brian suggests let's keep this conversation public, that was my first aim formerly. If you feel like the topic you want to discuss are sensible or you wanna keep them by yourself drop me a line (you can send messages privately).

Regarding the transformation I agree, it's a tough cookie. But what a delicious filling.

It may be "difficult" to introduce foreign material in it but you have chance to directly integrate the dna into the genome or to keep it episomal.

In this article http://goo.gl/iZPFWP transformation procedures are adressed. Well, just conjugation.

In this case I would always suggest to perform genomic integration, as it is much stable and less prone to diffusion.

@Dennis It definitely looks interesting from the setup point of view but it looks even more promising if somebody would like to use it to setup real production of molecules or for bioprocess development. These bacteria are commonly used in wastewater treatment, nonetheless as they are GRAF they are used as supplement in animal feed.

Apparently, but I should look better into that, they have some kind of stimulant effect also on plants.

Applications are p[lenty, just by using a wild type organism. But I am more interested in what you could actually produce by using it as a chassis for synthetic biology. Potentially they could grow on lignocellulosic biomass derived sugars, or express extracellular proteins to degrade cellulosic compounds.

They can live off of methanol, that you could synthesize cheaply and also integrate their diet with CO2 ans light.

Again would be awesome to find somebody with lab experience on this subject and delve into the details :)

Or come up with a project on this group and develop it further, why not?

Best,

Fede

[Brian Degger]

I'm pretty sure I have some of them in my winogradsky column.. (4.5 years old now) 

Once I have a safe place to open it, I will. 

As it is it sits on a shelf doing its thing. 

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[Katherine Gordon]

Thank you

On Nov 16, 2015 6:53 PM, "Brian Degger" <brian....@gmail.com> wrote:
>
> Katherine,
> A lot of us are interested in longevity(or aging well) ....so ask some questions.

>I was wondering if any of you are familiar with the current situation with the scientist in Siberia who identified a new strain of bacillus calling it simply bacillus-f and which has been used on crops to dramatically increase size health and yield? Also bacillus f injected into geriatric female mice has caused them to become youthful and have litters of babby mice...so the scientist injected himself with the bacteria two years ago I have heard only that he has not suffered from cold or flu and seems to have more energy, he appears to be in his early 60,s.  Nothing seems to have been published about him lately...

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