Anybody working on Lyme Disease?

[Adam Levine]

Hi everybody,

 

This is a really bad year for lyme disease, i'm curious if anybody is working on anything related to  Borrelia burgdorferi sensu stricto^[? 

Adam B. Levine

[Phil]

It would be nice to have a reliable test for Lyme.  Some issues that need to be addressed:

- What cell types does the bacterium inhabit?  In particular, which cell types does it hide out in while a patient is on antibiotics?  What is the best area to sample for a Lyme test?

- What would be a good PCR test to use that would detect all the known varieties of Lyme with a single test?

Another good project, en route to developing an RNAi-based therapy, would be:

- Identify sequences of B. burgdorferi that lie in essential genes, and that don't have homology with human genes.

[Adam Levine]

The woods of Northern California seem to be quite the hotbed of tick/lyme activity this  year.  My parents have lived out there for 28 years and gotten maybe 2 tick bites each in that time, no occurences of lyme.  So far in 2012 there have been hundreds picked from clothing, dozens of bites, and one confirmed & treated case (my mother).  My wife is currently getting blood drawn for the $260 basic lyme test from igenex.com that has a 5-40% chance of false negative.  

Happy to answer any questions about ticks, patterns or biome info from an observational perspective, but I'm not going to have too much to contribute on the technical side. 

Thanks for looking at lyme.

Adam B. Levine

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[rwst]

On Monday, July 9, 2012 6:49:36 PM UTC+2, Phil wrote:

It would be nice to have a reliable test for Lyme.  Some issues that need to be addressed:

- What cell types does the bacterium inhabit?  In particular, which cell types does it hide out in while a patient is on antibiotics? 

None and none. It completely lives in extracellular space, fortunately, but appears quite mobile.
 

What is the best area to sample for a Lyme test?

After infection, the wound. After months, it gets diffcult.

- What would be a good PCR test to use that would detect all the known varieties of Lyme with a single test?

That is to be seen. Promising would be liquor but that's not for the amateur.
Maybe you get traces of bacterial DNA in the blood but you don't know which genes. Only a professional study can determine that (except when sequencing gets really cheap or maybe a B.burgdorferi microarray is available)

Regards,

[Nathan McCorkle]

On Jul 10, 2012 2:58 AM, "rwst" <ra...@ark.in-berlin.de> wrote:
>> - What would be a good PCR test to use that would detect all the known varieties of Lyme with a single test?
>
>
> That is to be seen. Promising would be liquor but that's not for the amateur.

Liquor as in drinking ethanol???

[rwst]

On Tuesday, July 10, 2012 12:46:25 PM UTC+2, Nathan McCorkle wrote:

On Jul 10, 2012 2:58 AM, "rwst" wrote:
>> - What would be a good PCR test to use that would detect all the known varieties of Lyme with a single test?
>
> That is to be seen. Promising would be liquor but that's not for the amateur.

Liquor as in drinking ethanol???

Ah that appears to be a Germanism, it's short for Liquor cerebrospinalis---cerebrospinal fluid (CSF).

8)

[Adam Levine]

If you don't mind my asking:

Did you not know you were infected until it was too late to treat comprehensively, or did treatment just not work?

Adam B. Levine
http://MindToMatter.org

On Sun, Jul 15, 2012 at 8:28 PM, scylla <st...@photofischer.net> wrote:

I am a complete noob to biohacking and PCR. As yet, I do not have a machine yet, but Lyme disease is what sparked my interest. I have been suffering through increasingly severe bacterial illness many years after being bitten by tick. Really, I am hoping to make headway with my own illness, but it would be nice if I were someday able to make contributions that may help others with late stage disease. I feel like I will be a long way off, but indeed, I am very much interested in taking the first few steps.

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[scylla]

Certainly don't mind. I did not know I was infected until recently. Currently, all that is known about my condition is that I am infected with multiple bacteria, and a lot of it. Lyme is a very likely suspect. Certainly do not want to say "that's what it is" prior to testing, but that's where my current main interest lies: diagnosis. In large part, since I've not been successful thus far convincing Dr's to do a more reliable (PCR) test when antibody tests turn up negative, I am interested in doing one myself, provided it's not such a difficult task. I am sure I'm wrong in that! And, as knowledge about my condition progresses, I'd sure love to delve into this even further to see what I can find.

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[Nathan McCorkle]

On Mon, Jul 16, 2012 at 3:57 PM, scylla <st...@photofischer.net> wrote:
> Certainly don't mind. I did not know I was infected until recently.
> Currently, all that is known about my condition is that I am infected with
> multiple bacteria, and a lot of it.

Are they in your blood, or some organ? (I'm asking to figure out how
easy it would be to get a sample of the bacteria)

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[Gavin Scott]

My understanding of the Lyme testing issue is that if you've been infected and then treated with appropriate antibiotics, then the spirochetes are supposed to be dead but apparently leave PCR-detectable bits of themselves laying around indefinitely, meaning that the PCR test can tell you that you did have an infection, but if they've put you through the 2-4 weeks of antibiotics then the PCR test is pretty much useless except as a confirmation that at one point you did have it. A positive PCR test after treatment will not convince anyone that you still have an active infection.

The regular (two-step) tests are supposed to have very good accuracy once you're past the first few weeks of an infection (IIRC).

About 10-20% of patients, and especially those who have experienced symptoms for a period longer than six weeks before treatment, have some degree of lingering symptoms known generally as "Post-Treatment Lyme Disease Syndrome" which behaves rather like an auto-immune response. Most people seem to get better (or at least improve) over time, but some have ongoing problems, which has lead to people who think they have "chronic lyme disease", something that isn't recognized by the medical community generally, but which prompted the movie "Under our Skin" (http://www.underourskin.com/) which is worth watching if you're interested in the subject.

It's a pretty scary disease if just from the ease at which you can get it these days if you live in an area that has a lot of the ticks that carry it (http://www.cdc.gov/lyme/stats/maps/map2010.html). It's been the #1 vector-borne disease in the US for quite a while now. The biggest risk seems to be a long delay before diagnosis as well as many possible incorrect diagnoses (MS, arthritis, etc.)

None of the above is intended to be medical advice of course.

G.

[Phil]

On Tuesday, 10 July 2012 02:58:44 UTC-4, rwst wrote:

On Monday, July 9, 2012 6:49:36 PM UTC+2, Phil wrote:

It would be nice to have a reliable test for Lyme.  Some issues that need to be addressed:

- What cell types does the bacterium inhabit?  In particular, which cell types does it hide out in while a patient is on antibiotics? 

None and none. It completely lives in extracellular space, fortunately, but appears quite mobile.

Negative.  It's a spirochete.  See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC257809/,
"Intracellular localization of Borrelia burgdorferi within human endothelial cells,"
and http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Mechanisms_of_persistence
for a list of other cell types that the Borrelia spirochete invades.

 
What is the best area to sample for a Lyme test?

After infection, the wound. After months, it gets diffcult.

Right; only the "after months" question is interesting.

- What would be a good PCR test to use that would detect all the known varieties of Lyme with a single test?

That is to be seen. Promising would be liquor but that's not for the amateur.
Maybe you get traces of bacterial DNA in the blood but you don't know which genes. Only a professional study can determine that (except when sequencing gets really cheap or maybe a B.burgdorferi microarray is available)

What I meant was, what would be a good set of PCR primers to use,
which would detect all known variants of Lyme but not other bacterial infections?
That is something an amateur could figure out, from the sequences for the different strains,
which are available in GenBank.  AFAIK it hasn't been done.

[Phil]

On Monday, 16 July 2012 16:52:28 UTC-4, Gavin Scott wrote:

My understanding of the Lyme testing issue is that if you've been infected and then treated with appropriate antibiotics, then the spirochetes are supposed to be dead but apparently leave PCR-detectable bits of themselves laying around indefinitely, meaning that the PCR test can tell you that you did have an infection, but if they've put you through the 2-4 weeks of antibiotics then the PCR test is pretty much useless except as a confirmation that at one point you did have it. A positive PCR test after treatment will not convince anyone that you still have an active infection.

The regular (two-step) tests are supposed to have very good accuracy once you're past the first few weeks of an infection (IIRC).

About 10-20% of patients, and especially those who have experienced symptoms for a period longer than six weeks before treatment, have some degree of lingering symptoms known generally as "Post-Treatment Lyme Disease Syndrome" which behaves rather like an auto-immune response. Most people seem to get better (or at least improve) over time, but some have ongoing problems, which has lead to people who think they have "chronic lyme disease", something that isn't recognized by the medical community generally, but which prompted the movie "Under our Skin" (http://www.underourskin.com/) which is worth watching if you're interested in the subject.

Okay, let me try to respond to this in a non-angry way.

There is scientifically little question that there is persistent Lyme disease.
There are many thousands of patients being treated by many Lyme specialists
who have persistent Lyme disease.  You can show they have Lyme antibodies;
you can detect the spirochete with PCR; you can examine their tissue
and find spirochetes (if you are very patient);
you can show that these reduce in number during antibiotic treatment
and then return when you stop treatment.
Most importantly, these patients degenerate terribly when taken off
antibiotics, but do well as long as they stay on antibiotics.

There are a small number of doctors, primarily Eugene Shapiro, Gary Wormser,
and John Halperin, who, for whatever reason, have devoted their careers
to denying that persistent Lyme exists.  These three doctors were authors on the
NEJM study "A critical appraisal of chronic lyme disease", and also on the IDSA report
on the subject, and also on the American Academy of Neurology (AAN) report.
Everything on the Wikipedia page claiming that persistent Lyme disease
does not exist can be traced back to these three doctors.
These same doctors also claim that Lyme disease is rarely found
in the United States, which is complete bullshit.

You could make subtle arguments that the patients who are labeled
as chronic Lyme patients do not all have B. burgdorferi infections,
or that they are suffering some kind of bizarre auto-immune disorder
resulting from a prior infection that for some reason responds to
antibiotic treatments.  But the bottom line is that Shapiro and Wormser
insist that patients should be taken off antibiotics after a month,
and the reality is that these patients need continued antibiotics,
whatever the etiology of their disease.

[Gavin Scott]

On Wednesday, July 18, 2012 1:41:41 PM UTC-5, Phil wrote:

Okay, let me try to respond to this in a non-angry way.

You can be angry if you like; you have a much bigger stake in the issue than I do :)

 

There is scientifically little question that there is persistent Lyme disease.
There are many thousands of patients being treated by many Lyme specialists
who have persistent Lyme disease.  You can show they have Lyme antibodies;
you can detect the spirochete with PCR; you can examine their tissue
and find spirochetes (if you are very patient);
you can show that these reduce in number during antibiotic treatment
and then return when you stop treatment.
Most importantly, these patients degenerate terribly when taken off
antibiotics, but do well as long as they stay on antibiotics.

Then I would think this would all be easy to prove with a well-designed double-blind study or two. Has this been done? While science in general tends to resist change due to the entrenched positions of those highest up in the hierarchy, there's nothing like a little (or a lot of) good evidence to change people's minds pretty quickly.

There are lots of researchers in the world, and especially if this is so obvious of an issue as you describe then it ought to be easy to resolve the issue. Even accounting for a few extra degrees of naiveté on my part, I find it hard to believe that there can be such a far-reaching conspiracy against recognition of the truth here.

I have no strong opinion or stake in the question. I remain curious about the subject having watched "Under our Skin" recently, and my fiance is writing a paper on Lyme Disease for school so I have had occasion to read the CDC pages and do a few literature searches to help find sources for her.

G.

[rwst]

On Wednesday, July 18, 2012 8:09:34 PM UTC+2, Phil wrote:

On Tuesday, 10 July 2012 02:58:44 UTC-4, rwst wrote:

- What cell types does the bacterium inhabit?  In particular, which cell types does it hide out in while a patient is on antibiotics? 

None and none. It completely lives in extracellular space, fortunately, but appears quite mobile.

Negative.  It's a spirochete.  See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC257809/,

OK. I stand corrected. This and the more recent
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3067508/
should be enough to establish persistence. The fact that it has evolved an iron-free
physiology should be in line with this, too (the other mechanism is to steal iron from
the host via strong siderophores like M. tuberculosis and others).
 

"Intracellular localization of Borrelia burgdorferi within human endothelial cells,"
and http://en.wikipedia.org/wiki/Lyme_disease_microbiology#Mechanisms_of_persistence
for a list of other cell types that the Borrelia spirochete invades.

What I meant was, what would be a good set of PCR primers to use,
which would detect all known variants of Lyme but not other bacterial infections?
That is something an amateur could figure out, from the sequences for the different strains,
which are available in GenBank.  AFAIK it hasn't been done.

Not so fast. I thought that only in Europe there were several different strains infecting
people?

Also, while it's easy to find genes specific to those strains, they may not be all expressed,
or while expressed may not be excreted or even accessible on the surface of the bacterium.
And if it is, how do you detect them if the bacterium is inside a host cell? Your antibody blot
may be the best bet that you have.

To optimize detection via PCR of persistent bacteria, one should probably learn from efforts
done with M. tuberculosis instead of reinventing the wheel.

Ralf Stephan

[Cathal Garvey]

should be enough to establish persistence. The fact that it has evolved an iron-free
physiology should be in line with this, too (the other mechanism is to steal iron from
the host via strong siderophores like M. tuberculosis and others).

Whoa, wait: Iron _free_? No Iron at all? That's pretty damned impressive! :D

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[Phil]

On Wednesday, 18 July 2012 16:14:39 UTC-4, Gavin Scott wrote:

On Wednesday, July 18, 2012 1:41:41 PM UTC-5, Phil wrote:

Okay, let me try to respond to this in a non-angry way.

You can be angry if you like; you have a much bigger stake in the issue than I do :)

What I'm angrier about is the Lyme Disease Wikipedia page.
It has three sections on chronic Lyme disease.  These are all written with
a very biased viewpoint, putting "chronic" in quotes, claiming that belief in
chronic Lyme is a "minority" opinion "not recognized by mainstream medicine"
that only a "small number" of doctors hold, and that "most insurance" will not
pay for continued treatment of Lyme.  In reality, most doctors who have Lyme
patients use continued treatment; the only doctors I've met who follow the IDSA
guidelines on Lyme are general practitioners who have little experience with it.

When I change the biased language to neutral, or write [citation needed]
after one of these unsupported claim, my edit is removed as being biased
language or as needing a citation!

I downloaded the references that are ited in the Wikipedia article to show that
there is no such thing as chronic Lyme disease.  There's about 10 of them.
They were published in different medical journals, and by committes from different
organizations, including the IDSA, the American Association of Neurology,
the NIH, and the "ad-hoc committee on Lyme disease", whatever that is.
And, guess what, it's just the same doctors writing the same stuff over and
over!  The key three doctors, who are listed as authors on every original
source and were on every committee, are Shapiro, Wormser, and Halperin.

I corrected some of the most-biased language, and added text pointing
out that all of the citations used to claim that chronic Lyme denial is a
broad medical consensus are actually written by the same people.
Two anonymous Wikipedia editors, "Novangelis" and "Mast cell",
revert my corrections minutes after I make them, citing Wikipedia
guidelines that fail to apply as justifications.  When I pointed out that
all of the arguments against the existence of chronic Lyme are made
by the same people, Novangelis retracted this as "not being neutral
point of view".  I restored it, and "Mast Cell" retracted it as
"inappropriate synthesis".  (I listed 8 different citations and observed
they were all by the same authors.  Mast Cell calls this "inappropriate
synthesis" because none of the articles themselves mention the fact
that they are all written by the same authors).

Additionally, Novangelis is the same Wiki editor who retracts
edits from the Aspartame page that are not biased in favor
of aspartame!  I became acquainted with the aspartame controversy
about 2 years ago, when I wrote a proposal to study the effects
of gut microbes on the safety of artificial sweeteners.  I found
that the approval process was highly influenced by lobbyists;
the articles cited by governmental bodies to claim
that aspartame is safe were written (often without
any conflict-of-interest notification) by staff scientists of the
companies producing aspartame; opposing studies were
simply ignored by the regulatory agencies.  ALL of the reviews
of the aspartame literature cited by regulatory agencies were
written by staff scientists for chemical companies.
Reading the reviews, they were heavily biased, taking
studies showing safety uncritically, but coming up with
convoluted counter-arguments against each study that
did not show safety, or simply ignoring those more difficult
to dismiss.

[Adam Levine]

That's a problem with Wikipedia, it's become a very entrenched culture in places.  Don't take it personally.

Adam B. Levine
http://MindToMatter.org

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[Gavin Scott]

Yeah, Wikipedia seems pretty hopeless if you have someone willing to fight for their position, and it's generally just not worth the pain to try to sway things in your direction. About the best you can do is to cause your "edit war" to get the attention of other editors which might result in some sort of compromise, but there's no guarantee that things will work out in the direction of "truth", let alone your own definition of the word :)

Here's a link to current and planned studies related to Lyme Disease, including those currently recruiting volunteers if you're so inclined.

http://clinicaltrials.gov/ct2/results?term=lyme

I did some more reading on the subject, and it sounds like the standard two-step test should really be at least 85% accurate in anyone who has been infected for any extended period of time. If you're not showing positive on these tests then my advice (which is worth nothing) is to consider carefully whether those results might be correct.

G.

[Nathan McCorkle]

On Jul 20, 2012 5:48 PM, "Adam Levine" <adamlevi...@gmail.com> wrote:
>
> That's a problem with Wikipedia, it's become a very entrenched culture in places.  Don't take it personally.
>

That's disgusting,  what can we do? We've got enough people who know when a citation is needed or when scientific bias is happening.we shouldn't stand idle

[Adam Levine]

It's unfortunate, but people who look for information on the internet can generally find a variety of opinions, Lyme is no different.  As to taking on Wikipedia to try and right this wrong, I guess we could but it's a question of what you want to spend your time doing.  Edit wars and e-penis contests aren't my favorite.

Adam B. Levine
http://MindToMatter.org

[rwst]

On Friday, July 20, 2012 2:50:18 PM UTC+2, Cathal wrote:

should be enough to establish persistence. The fact that it has evolved an iron-free
physiology should be in line with this, too (the other mechanism is to steal iron from
the host via strong siderophores like M. tuberculosis and others).

Whoa, wait: Iron _free_? No Iron at all? That's pretty damned impressive! :D

It is, and so I looked a bit longer at this claim. PMID 9353077 has support for a Fe-SOD in
B. burgdorferi but they didn't try if the same enzyme works with Mn. Then there is PDB 2pyb
which would be a clear counterexample if the paper would have been published by now. The remaining hits in the 1250 gene B. burgdorferi proteome are five putative enzymes where some homologue in other species has iron ions or Fe-S clusters as cofactor. So, even if the claim may not 100% true, which is unclear, it is pretty close.

[Petfixer71]

The newest lyme detection test in Vetrinary med...see link below:

 
http://www.antechdiagnostics.com/Main/AntechNews/63.aspx

On Saturday, July 7, 2012 12:58:31 PM UTC-4, Recovering Salesman wrote:

[Phil]

On Friday, 20 July 2012 18:18:43 UTC-4, Gavin Scott wrote:

I did some more reading on the subject, and it sounds like the standard two-step test should really be at least 85% accurate in anyone who has been infected for any extended period of time. If you're not showing positive on these tests then my advice (which is worth nothing) is to consider carefully whether those results might be correct.

One problem is that the data that comes out of these tests is not "positive" or "negative", but (for example) stain densities in seven different lanes.  I have ambiguous results; what does that mean?  Another is that the tests are less reliable for someone who's been taking antibiotics - they generally kill off the most-accessible organisms, but may leave a reservoir hidden inside cells which will not show up on PCR.  Sampling synovial fluid is supposed to be more reliable, but doctors don't like to do that.  They prefer using blood or urine because these are accessible, not because they work.  No one knows how long you need to go off antibiotics before a PCR test, and it may be quite painful to do so.  Additionally, if you go off antibiotics for a PCR test, you may find that those antibiotics no longer work for you when you resume them.

Possibly a bigger problem is that there are a variety of bacterial infections communicated by ticks, and there's little reason to think that we've enumerated them all. This should change in the next few years, if someone does a metagenomic study of wood ticks. Someone did one metagenomic study of wood ticks, but they were looking for known organisms rather than doing assemblies and looking for unknown infectious bacteria IIRC.

A lot of patients have mysterious diseases that clear up under antibiotic administration.  These often get classified as Lyme, because they co-infect with Lyme and so the patient has Lyme antibodies, or just because bacterial infections generally cause fatigue and chronic pain.  Then someone will argue that these patients don't have Lyme, and therefore should not be on antibiotics.  This is moronic.  The question is not what disease they have; the question is how to make them better.  This is one reason why double-blind tests are kind of pointless in this case.  First, I don't care whether the effect is a placebo effect.  If it works, it works.  Second, double-blind tests assume that you can accurately categorize your  patients into those who have the disease, and those who don't, and that EVERY SINGLE PATIENT who has the disease responds in the same way to treatment.  Even those with Lyme are going to all respond differently; and your set of "Lyme patients" is certainly going to contain a lot of people with other infections, and a lot of hypochondriacs.

I could write an article on why the standard double-blind test is so often misleading.  If you're testing a treatment, or a drug toxicity, typically some subset of patients has a positive or negative response, based on environment or genetics.  If 10% of your population has a set of SNPs that dictates a negative response, a standard double-blind test will be cited as "proof" that no such response exists, because the hypothesis that all patients with this condition have a negative response will most likely be rejected with 95% certainty.  This is the case for hyperactivity in response to certain food colorings, which the medical establishment vociferously proclaimed to be a myth for 40 years, until recently it was shown that the effect is strong if you restrict yourself to looking at certain types of food dyes and patients with certain SNPs.  (You have to account for multiple hypothesis testing when dealing with restrictions, of course.)

[Phil]

On Sunday, 22 July 2012 12:08:10 UTC-4, Petfixer71 wrote:

The newest lyme detection test in Vetrinary med...see link below:

 
http://www.antechdiagnostics.com/Main/AntechNews/63.aspx

It makes me want to scream every time I see areas where veterinary medicine is far ahead of human medicine.  About 10 years ago, I had a leg nerve injury that confined me to a wheelchair, and my doctor said, "There's no cure for this, unless you're a horse..."  I might still be in a wheelchair if I hadn't illegally used veterinary medications.

[Cathal Garvey]

Given that lots of senior editors on Wikipedia use revert-bots to revert
a broad class of edits on principal (the reasoning being: if you are a
good contributor, you'll edit-war the bot, and it'll cave), I'm pretty
skeptical of Wikipedia's odds on issues like this.

To win *any* battle of fact against fancy, you've got to have someone on
your side with advanced privileges on Wikipedia, so they can lock out
badly programmed revert-bots and manchild "editors".

[Nathan McCorkle]

What vet meds cure nerve damage?