Science

Hi friends. First and foremost, I want to wish everyone reading this my best wishes during these challenging times.

After spending 15 years working in tech as a software engineer + exec and eye-opening psychedelic experience, I've decided to pivot my life into a new direction: documenting my journey to self-learn genetic engineering and the development of a new product that helps mankind.

It's early days, but I have a working site and social media up here if you'd like to learn more: https://everymanbio.com/ + https://www.instagram.com/everymanbio/ 

One of the projects I'm using to concentrate and advance my learning is to engineer an organism and use it to produce a valuable compound en masse. The idea isn't new; a couple of youngsters recently utilized this technique to create a $200M company that produces hydrogen peroxide with yeast.

I'm enthralled by the idea of using something like Saccharomyces cerevisiae or e.coli to produce a highly valued compound at low-cost and reasonable biological efficiency. 

My question is this: how can I use public data sources to identify potential targets for biosynthesis? Given I can code and things like crawling, big data collection and analysis are well within my wheelhouse, I can't help but to think of the value it might offer to me and the community in narrowing in on which compounds would be best suited for biosynthesis from am GMO'd organism.

But! I don't know what I don't know and I could use some insights into the following:

• What features or attributes make a compound a feasible target for biosynthesis? What makes it completely infeasible?
• What data sources can be used to search and assess compound targets? I'm looking for ways to both quantify high-demand /valuable compounds and compounds that are suited for biosynthesis.
  

Ideally, I'd like the end result of my analysis to capture something akin to:
Compound Name | E.Coli Synthesis Feasible? | Yeast Synth Feasible? | Market Value | Production Difficulty | Metabolic Complexity | Compound Use (Medical, Industrial, etc)

I realize this is probably fairly wide in scope of a question, but I hope to at least get the conversation going and to be pointed in the right direction.

If you'd like to reach out to me directly to discuss the idea or explore a collaboration, please feel free to email me josh@everymanbio.com

With much gratitude,

Josh McGinnis, Founder of EverymanBio

https://everymanbio.com

https://www.instagram.com/everymanbio/

  

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https://www.theguardian.com/science/blog/2011/jun/21/scientists-make-lsd-from-microbes

Hint: it didnt work.

 

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https://www.electronicdesign.com/technologies/test-measurement/whitepaper/21133268/advanced-diy-project-replicates-costly-biology-highvoltage-test-tool

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On 7/25/20 9:01 PM, Daniel C. wrote:
> Has anyone put together a system like this?  What products / brands have you had success with?  I'm particularly interested in
> pump reviews.

I have not, but there are hackaday articles about repurposing refrigeration pumps to do vacuum.  They talk about ongoing vacuum
oil maintenance needed, etc., so that's your requested review.   To simply speed filtering, a 90% vacuum would be enough.  You
could make a system with pressure switch and relays to turn on/off a tiny fridge compressor.  The pressure switch could be one of
the pressure ICs available, or for completeness, an Industrial Pressure Sensor that includes switch contacts and pipe fittings.
The price of the Industrial pressure switch is about $36 from Mouser and a Melexis IC is $12.  For $12 you get a 5 volt output and
some complicated way to adjust the trip point that will require programming a microcontroller and then you'll need relay drivers
or a SSR for another $10 in parts and loads of design time, so the Industrial pressure switch for $36 looks good for a one off.

Running a small fridge compressor this way would not strain it, (unless you left the vac valve open all weekend maybe...).

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Hi Frank... thats what I was saying... the boj Ko post seems not appropriate for this DIY TPE conversation. I think it was posted in the wrong group.

On Tuesday, July 14, 2020 at 12:52:00 AM UTC-5, Frank Garcia wrote:

I'm spacing out on boj ko post. is that my post?

On Tuesday, July 14, 2020 at 1:50:27 AM UTC-4 Frank Garcia wrote:

Dale,

 Are you saying the discussion about TPE is not appropriate for DIY Bio?

On Monday, July 13, 2020 at 10:19:52 PM UTC-4 dale wrote:

Frank are you feeling any younger yet?

Still planning a 2nd plasma donation?

I have started researching Epigenetic age tests but have not had much free time recently.

Does the boj Ko post belong in a different group?

On Wednesday, July 8, 2020 at 12:49:19 PM UTC-5, Frank Garcia wrote:

true. good advice. i did not have tests performed party due to expense. Not sure how many of you are the the US, but here even if you have so called insurance, it doesn't cover testing beyond the standard old blood tests . If anyone has suggestions for how get relevant biomarker tests cheaply please let me know.

On Wednesday, July 8, 2020 at 12:28:19 PM UTC-4 dale wrote:

So Frank... do you feel younger today?

Did you get any kind of biomarker or epigenetic age test before?

I would not look for another TPE too soon. The blood center probably requires 28 days for important safety reasons (they should know being that blood is their business).

I don't think the conboy article mentioned any dose dependent or time requirements. To me it seems if you flush 25%  or even 10% of the old garbage each time, it should still be the positive effects they claim, but cumulative.

My household doesn't care if the trash goes out all at once or in 4 or 5 trips... just so it goes :-)

On Tuesday, July 7, 2020 at 3:53:14 PM UTC-5, Frank Garcia wrote:

Quick update about obtaining TPE.

So I went to the blood center in NYC and donated 800 ML of plasma which they replaced with saline but no albumin. It was a TPE process like in the paper I posted here but with only about 25%, half of the ideal 50%, plasma dilution and no added 5% albumin. They will not take more unfortunately. and i have to wait 28 days to donate again.  I'm thinking there should be dose-dependent benefit?

I thought I would be able to do the same with a different blood donation org like red cross who wouldn't know I just donated but they have no locations in NYC and they only take plasma donation from people with blood type AB. I have O. Looking for other blood banks that take donations.

On Friday, July 3, 2020 at 1:24:23 PM UTC-4 Frank Garcia wrote:

Gary,

Right, the point is you do not take whole blood, just plasma, otherwise you wouldn't be able to take the needed amount of plasma.

Thanks for pointing out the PRP. I missed that. I'm going to have to back and read again to see if they consider platelets to be the source of some of "the bad stuff".  However they also say that their procedures is the equivalent of TPE which does not take platelets, right?

On Friday, July 3, 2020 at 8:42:16 AM UTC-4 Gary Dale wrote:

Thanks Frank, I think you're right.

I reviewed the conboy article and their quote: "a single TPE yielded functional blood rejuvenation" says you don't need a whole blood donation.

They seem to believe their NBE/TPE yielded "significant dilution of autoregulatory proteins that crosstalk to multiple signaling pathways".

Apparently  the centrifuge step to separate out the plasma does not remove ALL particles from the plasma.

But I think they are removing platelets with the plasma because they refer to the plasma as PRP:

"Specifically, we performed a "neutral" blood exchange (NBE) by replacing the platelet-rich-plasma (PRP), fraction with physiological saline"

On Thursday, July 2, 2020 at 9:27:30 PM UTC-5, Frank Garcia wrote:

Not exactly that way Gary. Plamsa is the the thing you want to eliminate, not RBC or platelets. in TPE, plasma is extracted and not returned. Also, the volume of plasma that is taken is replaced with saline solution. this and the return of the rbc allows for extracting significantly more plasma than with whole blood donation. and the goal is to lose up to 50% of plasma.

On Thursday, July 2, 2020 at 3:47:40 PM UTC-4 Gary Dale wrote:

I am no expert but seems to me (as a DIYBIO enthusiast) that TPE might not produce a complete a flush as a plain old blood donation.

MY understanding of TPE is that the plasma is separated out by centrifuge separating ALL heavy particles....blood cells and junk to be returned to the donor, thus putting all the particulate garbage back in to you... not actually ridding it from the body as in a blood donation  :-)

COMMENTS...IDEAS... CORRECTIONS...?

On Thursday, July 2, 2020 at 12:00:50 PM UTC-5, Frank Garcia wrote:

Can i summarize what we've all said here about testing this way:

1. we want to know if an intervention is effective

2. so we want to test rejuvenating changes in physiology

3. real benefit should be detectable and demonstrable with

                - increases in physical capacity

                - improvements in metabolic and other physiological end products and systemic biomarkers

                - changes in gene expression marked by epigenetic changes

4. thus to have a good sense of the effect an intervention has had we can't use just one type of test. We should employ multiple types of tests that include a selection from at least these three categories

                - exercise capacity, BMI, resting heart rate, blood pressure, sleep patterns, bone density, etc.

                - molecular marker of glucose, cholesterol, inflammation, GRF, CRP, fibrosis, etc

                - epigenetic markers such as methylation levels and other gene expression markers, mitotic competence

On Wednesday, July 1, 2020 at 3:40:10 PM UTC-4 Raph N wrote:

https://nintil.com/epigenetic-clocks

On Wed, Jul 1, 2020, 19:58 Raphael Nicolle <rap...@gmail.com> wrote:

Yes this is what I think. Hopefully commercial applications democratize soon enough :)

On Wed, Jul 1, 2020, 19:37 Frank Garcia <fgarc...@gmail.com> wrote:

sounds like the epigenetic tests may in fact reflect physiological status not just passage of time. i'm going to read up on this a bit. 

On Wednesday, July 1, 2020 at 1:27:58 PM UTC-4 Raph N wrote:

• Epigenetic age test is an aggregation of hundreds of methylation sites in the genome, tracking change in expressions of many genes (involved in multiple pathways then).
• It correlates extremely well with chronological age (r>0.9).
• BUT it is amenable to some interventions which causes a lower epigenetic age, which also matches other biomarkers you cite such as fasting glucose, senescent cells, mitochondria output,... 
• In fact most* hallmarks of aging, as measured by other means, do correlate with this epigenetic age result as well, whether it matches chronological age or it is substantially lower (or higher for that matter).
• We can also reset the epigenome using a set of genes (the 4 Yamanaka factors), which gives a cell that is biological as young as we want (all the way to embryonic), with an epigenetic age of 0, and a fully functional embryonic phenotype. Or whatever the "clock" was stopped at.

I don't know what you conclude from these facts, but personally, I conclude that we have a serious contender to a very accurate age marker.

*I say most and not all because the rest haven't been formally studied, not because they do not correlate to epigenetic age as well. 

On Wed, 1 Jul 2020 at 18:16, Frank Garcia <fgarc...@gmail.com> wrote:

Actually it isn't chronological age that we want to measure. we know how old someone is. we want to measure biological age. and that is contributed to by a huge number of variables. biological age means health. think of this as a myrid of axis or spectrums gradually change as we age, from the elasticity of your blood vessels, the levels of metaloproteinases you produce, the amount of senescent cell populations in your body, how much  advanced glycation end products you have accumulated, hormone levels such as growth hormone, androgens, and klotho, just to name a few out of thousands. moving the needle backwards on those axes makes you younger. But can any single test or type of test give an accurate reflection of that?

On Wednesday, July 1, 2020 at 12:26:15 PM UTC-4 Raph N wrote:

That's a good point, what is rejuvenation? 

For me it's the actual "running back" of the body clock. To qualify as rejuvenation, an intervention should be able to postpone indefinitely aging if repeated sufficiently enough. So it's different than just doing exercise and be in better shape for example.

I have a problem with general biomarkers like insulin sensitivity etc,... The reason is basically this: https://michaellustgarten.com/2020/06/26/blood-test-analysis-in-a-100-year-old-subject/ If you look at the blood work of this subject, it would quite good even for a 40 year old. and yet, I'm certain if I see this subject, I will know right away he/she is definitely NOT a 40 years old. 

So we need a biomarker that is as closely related to chronological age as possible. And, for all its potential implementation issues, epigenetic age is so far the closest to the mark, with a correlation of 0.94 or even better for the latest peer-reviewed iterations. That's fracking good. And it's not just a "single" biomarker, it's a composite from hundreds of methylation sites across the genome, corresponding to hundreds of different gene expression changes.

Now the mirror test is a good one, but it will take a pretty good effect to show up with confidence, something I'm not sure TPE would do (or we definitely would have heard about it).

Anyway, multiple approaches are good, and I agree those fancy tests are expensive still :)

On Tue, 30 Jun 2020 at 21:36, Frank Garcia <fgarc...@gmail.com> wrote:

I guess we need to define rejuvenation then. the biomarker tests in the experiment each measures one tiny piece of the physiological state which, depending on the direction in which the marker changed, indicates a physiological state that more closely resembles that of a younger organism. I'm not sure (maybe i'm wrong) there is a universally accepted definition of rejuvenation. and there certainly isn't any single market that proves rejuvenation. It's simply too complex for that to ever be the case. It's more like pick your basket of markers of aging and test them over a period of time and see which way they are heading.  I personally think any markers of rejuvenation has to include those that measure the physiological dirvers of age -related disease and deterioration such as insulin sensitivity, fibrotic markers, resting heart rate, muscle stem cells, mitochondrial markers, cholesterol trajectory, cardiac output efficiency, C-reactive protein, just to name a few out of a million.  In the study, muscle anabolism vs catabolism is in fact a good aging biomarker

On Tuesday, June 30, 2020 at 2:20:11 AM UTC-4 Raph N wrote:

The problem with the biomarkers used in the experiment is that they can't prove rejuvenation.  For example we know exercise improve lots of biomarkers, yet it does not rejuvenate you, or you could exercise your way to immortality. 

As far as we know epigenetic clock is the best marker of biological age. 

Raphael <rap...@gmail.com>

On Tue, Jun 30, 2020, 01:50 Frank Garcia <fgarc...@gmail.com> wrote:

I don't know too much about the epigenetic tests however it might be useful for you to take a look at the biomarker tests that were used in the experiment that I posted which started this discussion. They did pretty rigorous testing of multiple systems and tissues to determine efficacy.

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