DIY longevity biology

[Anton Kulaga]

Hello,

when we ( "LIttle mouse" crowdfunding team) gave an interview to H+Magazine we were asked about DIY longevity biology. I quote the answer here as it may be useful for those of you who are going to conduct DIY lifespan tests and do other research in biogerontology.

Q: Some of our readers are DIY self experimenters and citizen science enthusiasts. Can you provide any advice or warnings about these substances?

Iryna: We plan to make public reports about the conduct of the study an online, to publish the design of the experiment, the choice of optimal methods of research that can help citizens better understand how conduct research in this area.

Anton Kulaga, Edouard Debonneuil: Do It Yourself biology is great! When it is done right it strengthens connections between professional researchers and citizen scientists where all parts benefit a lot. So we support DIY movement, we even organize DIY workshops in Kiev and provide biology training as one of the perks. The main advice here is to keep contacts with professional scientists in the field of your citizen science research. Clearly, not all labs are friendly to DIY activists, but the world is huge and you can find labs that will be eager to help you with your research, and vice versa find ways for you to help them.

In ageing research and in lifespan tests in particular there are several groups trying to do something. One of them is coordinated by the LongeCity forum, a quite active forum  but many of its activists do experiments with… a huge room for improvement in scientific quality. We have to warn that lifespan experiments are not as easy as they may look like, many details count and it is not just buying mice and feeding them with some drugs. For example, lab lifespan tests usually involve many animals in both control and test groups and the strains are important. A first step is to look at current interventions databases and look at interventions done on mice (or animal of your interest); one of such databases is created and maintained by Denigma project (http://www.denigma.de/lifespan/interventions/ ).

The easiest thing is to reproduce experiments of others, as dosages and protocols are already designed there. Even to reproduce experiments it is desirable to write to the researchers that performed them as many details, some of them potentially important, are not in papers.

To get fast and reliable experiments it is useful to buy aged animals from a specific strain, but depending on countries such animals might be restrained to animal research facilities with very restrictive agreements. DIY activists cannot afford having many animals so you should cooperate: fund labs to conduct lifespan tests for you, create joint vivariums or distribute your tests among many people (but be aware that distributed lifespan tests might not be well trusted and therefore be hard to publish). You have to make sure that treated and control mice are treated identically, so double-blinded tests are highly desirable.

(source H+Magazine, http://hplusmagazine.com/2013/10/14/i-am-a-little-mouse-and-i-want-to-live-longer-support-crowdfunded-longevity-research/ )

[Reason]

The mice folk succeeded in hitting their fundraising goal, so good for them:

http://www.indiegogo.com/projects/i-am-a-little-mouse-and-i-want-to-live-longer

Also worth noting that the fundraising for the latest Longecity crowdfunded research project (a small chunk of the goal of allotopic expression of critical mitochondrial genes, so as to remove that contribution to degenerative aging) is going well: $5k down, $2k to go, with these donations matched $2 to $1 by Longecity:

http://www.longecity.org/forum/topic/65889-longecity-research-support-2013-mitochondrial-gene-therapy/

There are also some peripherally relevant medical research projects on Microryza these days, some of which seem to be doing well - largely a matter of the researcher's ability to network I think, with Microryza providing the infrastructure. Still a way to go before it hits Kickstarter-like network effects:

https://www.microryza.com/projects/can-modified-adult-stem-cells-reverse-neurological-pathologies
https://www.microryza.com/projects/can-we-use-3-d-printing-to-engineer-organs-affordably
https://www.microryza.com/projects/developing-a-new-treatment-for-neurodegenerative-diseases

Speaking of Kickstarter, it has to hurt that it's easier today to raise $35k for fiction about the near future of longevity science than it is to raise funds to actually get the longevity research accomplished. On balance people like their bread and circuses, but feel next to no urge to contribute to the scientific research that makes their lives so much better than those of their recent ancestors.

http://www.kickstarter.com/projects/1956082973/the-last-generation-to-die-a-short-film

Reason

On 10/14/2013 08:36 PM, Anton Kulaga wrote:

Hello,

when we ( "LIttle mouse" crowdfunding team) gave an interview to H+Magazine 
we were asked about DIY longevity biology. I quote the answer here as it 
may be useful for those of you who are going to conduct DIY lifespan tests 
and do other research in biogerontology.

(source H+Magazine, 
http://hplusmagazine.com/2013/10/14/i-am-a-little-mouse-and-i-want-to-live-longer-support-crowdfunded-longevity-research/
 )

[Joe Gorse]

Reason,

It is not sufficient to merely compare the two categories of efforts, one scientific and the other fiction storytelling, based purely on the technical longevity value. The reasons for why the fiction creative effort reaches its fund raising goal in this case might just be that they use media well and are simply focused on telling a compelling story, whereas scientists tend to often pretend to forgo such details as irrelevant--ironically just as most folks go through their lives without ever thinking critically about whether or not they would like to opt-in to death-by-aging. The Last Generation To Die kickstarter addresses the larger current need for common ground in having that conversation about the need to die-by-aging, which is no small part of the current longevity scientist's challenge in bringing his post-paradigm-shifted message to the funding agencies, the public, and investors.

Some folks I know have contacted Tim Maupin, the director of the The Last Generation To Die, and he appears to be legitimately interested for the right reasons. As such, if there were a sufficiently high priority scientific project that we might recommend as a group, I'll bet we could get Tim or some of his associates to help with the media production. That would really be the best of both worlds.

Cheers,

Joe

[Reason]

Ah, and I see that SENS Research Foundation folk are answering questions about the modest-sized mitochondrial gene therapy project hat is presently being crowdfunded - it's interesting stuff, worth a look for the rest of it, not just the quote below. After all, there are many people on this list who, given the lab support and connections provided by an SRF-like group, could be doing work in the medical life sciences that is just as cutting edge as this:

------------------------

http://www.longecity.org/forum/topic/65892-mitochondrialgenetherapy-questions/

Q: So why did you pick CyB and ATP8 as the two genes to work on here? Was that a fortuitous happenstance in terms of a suitable source of mutant cells to work with?

A: This is one of my favorite questions because we've spent so much time and effort figuring out which genes to focus on.

One reason is that these may be both the easiest and hardest genes to achieve efficient import with. CyB has a reputation (whether or not it is deserved is a matter for some debate) in the field of being the most difficult and hydrophobic protein to import into the mitochondria. It is one of the bigger mitochondrially encoded genes, so at the very least it is a challenge. ATP8, on the other hand, is tiny and so may be considered the easiest to import. Thus we've set ourselves a task that spans the range of challenges that we think we'll encounter.

The second reason is that, strategically, OxPhos complexes III and V are the most interesting for proof of concept rescue of the entire mito genome. The reason is that they have the fewest genes that are encoded by the mitochondria. Complex III has only CyB (and thus ONLY CyB is needed to rescue the entire complex) and Complex V has only 2: ATP6 and ATP8. So if we want to study functional rescue of entire complexes then III and V are the easiest.

The last reason is a common one in biology: the availability of useful tools for study. Mitochondrial mutations are relatively rare, difficult to create artificially, and the vast majority of naturally occurring mutations (in the protein coding genes) are partially functional point mutants. These are messy to study because they still produce protein and the proteins they produce are simply less functional than the wt version. Thus the phenotypes are mild compared to null mutations. We have worked with many different cell lines derived from patients in the SRF Research Center. We have a difficult time telling the difference (functionally) b/w point mutant cells and wt cells. The only way we can do it is with the difficult and expensive oxygen consumption assay. All our other assays are essentially useless in these cells. We have found (fortuitously as you guessed correctly), truly null cell lines for ATP8 and CyB. Researchers have shared their heteroplasmic mutant cell lines of these two genes with us and we are working on making them perfectly homoplasmic. They are already very useful in our experiments. The other tool we have is that we have antibodies that work against these two proteins. For some reason this seems to be rare for mito encoded proteins. No idea why. We have an excellent antibody against ATP8 that we had custom made for us and we tested many commercially available CyB antibodies and finally found conditions under which we get one to work passingly well.

------------------------

Reason

[Reason]

I'm not opposed to dollars for advocacy, or even dollars for general
raise-all-boats awareness, I'm just bemoaning the nature of this world,
in which people seem extraordinarily reluctant to actually fund
research. I think it's more than just a matter of the (not particularly
accurate, I think) stereotype of scientists being terrible at
presentation and marketing. Anything but research will do better as a
fundraising project, despite the fact that the research is what gets the
job done - it has to be funded at some point, some collection of
someones has to pull the trigger and hand over the dollars.

Reason

On 10/15/2013 07:34 AM, Joe Gorse wrote:
> It is not sufficient to merely compare the two categories of efforts, one
> scientific and the other fiction storytelling, based purely on the
> technical longevity value. The reasons for why the fiction creative effort
> reaches its fund raising goal in this case might just be that they use
> media well and are simply focused on telling a compelling story, whereas
> scientists tend to often pretend to forgo such details as
> irrelevant--ironically just as most folks go through their lives without
> ever thinking critically about whether or not they would like to opt-in to

> death-by-aging. The Last Generation To Die<http://www.kickstarter.com/projects/1956082973/the-last-generation-to-die-a-short-film>kickstarter addresses the larger current need for common ground in having

[Mega [Andreas Stuermer]]

Hi!

Found this: 

http://nextbigfuture.com/2013/09/mitochondria-rejuvenation-in-mice-gave.html

Unfortunately there does not seem to be a paper about this anywhere.... Maybe someone here knows more about it?? 

[Cathal Garvey]

According to the linked New Scientist article it wasn't in a paper, it
was presented at a SENS conference.
So, expect peer review and paper sometime in future. Until then, take
with a pinch of salt! :)

--
Please help support my crowdfunding campaign, IndieBB: Currently at
23.9% of funding goal, with 26 days left:
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W: http://indiebiotech.com

[Reason]

You might look at these posts for more context on the subject of TFAM and mitochondrial repair.

https://www.fightaging.org/archives/2012/10/what-happened-to-protofection.php

https://www.fightaging.org/archives/2013/04/an-update-on-protofection.php

Reason

On 02/15/2014 03:20 PM, Cathal Garvey wrote:

[Mega [Andreas Stuermer]]

Ok. But this sounds too good ;)

Transfect some cells that produce a mitochondrial protein. The protein is released into the bloodstream. The protein then enters the cells and due to its mitochondrial localization signal enters the mitos and does its job. Forever young :D of course not, as there still are other mitochondrial genes you'd have to replace this way.

[Reason]

On 02/15/2014 04:21 PM, Mega [Andreas Stuermer] wrote:
> Ok. But this sounds too good ;)
>
> Transfect some cells that produce a mitochondrial protein. The protein is released into the bloodstream. The protein then enters the cells and due to its mitochondrial localization signal enters the mitos and does its job. Forever young :D of course not, as there still are other mitochondrial genes you'd have to replace this way.
>

In the original protofection methodology TFAM is only a vector, a way to
deliver an attached chunk of mitochondrial genome, and thus provide
replacements for damaged mitochondrial genes that have overtaken cell
mitochondrial populations because they are selected for in mitochondrial
cellular dynamics, despite being harmful to the organism. You can
replace the whole genome at once this way, which is why it is
interesting. The gene-by-gene allotopic expression approach of SENS is
more work, but has the upside that it absolutely fixes the problem
forever going forward. There is the nagging suspicion that delivering
new mitochondrial genes will have only a short term benefit unless you
get rid of the old damaged ones completely (whole separate topic of how
to clear and replace mitochondria safely), because if you don't then the
same mechanisms that caused clonal expansion of the damaged
mitochondrial genomes will still be operating.

I'm told other teams have had trouble replicating protofection in the
years since then, but there are other mechanisms that work or might work
or are in some stage of being made to work to deliver new mitochondrial
genomes to mitochondria. Or even deliver whole mitochondria, since
apparently there are proteins you can attach to a mitochondrion that
encourage a cell to engulf and adopt it.

The principal protofection researchers have found that TFAM in and of
itself has enough of an effect on mitochondria / metabolism / whatever
that it makes more economic sense under the present regulatory situation
to pursue that as the basis for a marginal therapy for LHON /
Parkinson's disease / whatever rather than the thing that you can't get
regulatory approval for, which is treating the "normal" mitochondrial
dysfunction that contributes to aging.

Even if you repair mitochondria and gain benefit, you're not forever
young. You still need to repair the other causes of degenerative aging.
Senile systemic amyloidosis in particular will kill you somewhere past
the age of 100 regardless of your mitochondrial status. All (seven-ish)
of the processes causing aging need to be addressed/repaired in order to
unlock radical life extension. Probably. Though I'd be surprised to find
that any of them can be ignored, given the clear links between these
processes and specific fatal age-related conditions.

Reason

[Mega [Andreas Stuermer]]

I agree. But, you gotta start somwhere. And mitochondria are a quite important issue.