Lyme disease, science, and society: Camp Other
Showing posts with label education. Show all posts
Showing posts with label education. Show all posts

Sunday, May 20, 2012

0 Commentary: 20/20 And Needing A New Focus For Lyme Disease

This past Friday, the ABC program, 20/20, aired a show on medical mysteries. Included in this show were segments on people who fly into a rage at certain sounds (misophonia), eat rocks or other unusual non-food items (pica), and one on a girl with Lyme disease who is speculated by doctors to have developed a condition known as foreign accent syndrome (FAS) due to being coinfected with Bartonella.

While I have sympathy for everyone dealing with such conditions and hope everyone who was interviewed for the show gets better, what I'm about to write isn't about their personal interest stories.

Instead, I want to discuss how the media portrays the strange and unusual case to get higher ratings while other stories and information about tickborne infections are either downplayed or avoided.

On Dr. Phil's show several weeks ago, a young model was interviewed - a photogenic young woman who was having partial seizures and self-medicating to treat her pain. While there is evidence that people with Lyme disease can experience seizures, these cases are considered to be in the minority. In Friday night's 20/20 show, a teenager in high school who contracted Lyme disease and Bartonella was speculated to have developed a condition known as foreign accent syndrome (FAS). This is a documented condition, and while I think more evidence is needed to provide a link between Bartonella as its cause in this instance - FAS is even rarer than seizures are.

These stories are getting aired because the media tends to want to focus on the strange and unusual in order to grab viewers' interest and get ratings. The delivery must generate buzz and be sensational in approach in order to get traffic and fixed stares. And this is exactly what the promos for Dr. Phil's show on the young model, Stephanie, tried to achieve - as well as promos by 20/20's on Elaina, the teenager with FAS.

Most viewers at home seeing these shows are watching it because of the weird factor. They see the promo and want to know more, perhaps with their own internal dialogue of, "Wow, that's weird, I wonder how that happens - and does this really happen or is it just made up?" or, "Gee, that's messed up - glad it's not me. But I'm curious, so I'll watch." Some people just have a thing for watching other people's problems in general, and segments like these appeal to their nature.

For those of us who suffer from a disease that is portrayed on television, the first thing that happens is praise. The initial comments from the Lyme disease patient community are congratulatory. They contain the good cheer of finally getting more recognition for what ails us, those of us who have been suffering with chronic Lyme disease and/or coinfections.

And then, the next round of responses trickle in from other patients - a second wave which is not as cheery as the first and criticizes the shows for picking out one narrow and possibly rare symptom and putting it in the spotlight while the rest remain in the darkness.

Then the real, serious criticism gets rolling in the third wave, which is about how these shows will question the afflicted about the true nature of their condition and whether or not they are "faking it". From the perspective of a number of Lyme disease patients, this criticism could be heard regarding the exchanges about Dr. Phil asking the model if she was faking her condition, and in his not arguing against Dr. Auerwater's position that chronic Lyme disease is not a verifiable condition.

Indignant responses fly. Suddenly, what began as a great show for spreading awareness has become a show where a number of people see the value of airing it - yet admit it fell short of their hopes for letting people know what Lyme disease and coinfections are really like and what impact persisting symptoms have had on people's lives.

People just like them. People just like the guy next door, who was mowing the lawn one week and playing soccer afterwards - and now can't make the walk to his mailbox, let alone get to work.

As I see it, there has to be more of an effort in the media to offer education about what Lyme disease and coinfections are from a scientific perspective, and educate people on the most common symptoms which people will experience. From a personal interest perspective, more people need to see how these conditions affect middle class working adults with children of their own.

With this education, more people would be able to relate to the people on the screen and be willing to look into the possibility that they might have a tickborne infection and seek medical advice and testing. They would at least be alerted to the possibility.

With the edutainment of the strange and unusual offered, there isn't enough there for the viewer to grasp the possibility that they, too, may be suffering from this disease - or to know what signs to look for in the future if they do come down ill with tickborne infections.

If someone sees the story of a patient with partial seizures or FAS, they may shrug off the story and not apply it to their own experience of having joint aches, muscle pain, headaches, and blurred vision, and say to themselves, "Thank god I have fibromyalgia and eye problems and not Lyme disease or Bartonella - this stuff is weird". And maybe their current diagnosis is correct. However, there's a chance it's not. In which case, they are better off having the knowledge so they can decide to investigate another diagnosis.

The strange and unusual won't help viewers relate what they see on the screen to their own situation. Truly spreading awareness means educating people on the symptoms for conditions one is most likely to see. It doesn't mean that there aren't exceptions or that unusual symptoms can't occur. It just means that what most people with a given condition experience what one expects to see and to get based on the majority of cases which have occurred.

One more point about the media's focus and where I think it should be - then I'll go:

Why is it that we can easily find these sensationalized stories about unusual symptoms about Lyme disease - but there's seemingly little television coverage of what seems to be the most costly case of Lyme disease in the country - the Lyme disease contracted by senior banker Ina Drew, who worked at JP Morgan Chase, whose absence from work due to Lyme disease led to those remaining in the office making decisions leading to a $3 billion trading loss?

Yes, you did not misread that. $3 BILLION.

You would think this story would be pretty sensational and the media would put this on 20/20 and other shows right away.

There is the personal cost of Lyme disease to the individual. This the media does well to portray to a certain degree. But then there is the cost to their family, their job, and society as a whole. This has not been portrayed that well. It needs to be.

 Image Credit: Peter Wolber


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Wednesday, April 25, 2012

2 Strange But True Facts About Spirochetes

Image: Kilauea Volcano
by Brian Snelson

I have a few strange but true facts about spirochetes to share which you may not know. A few are ones I have shared here before  - but most are not something about which I've already written. What you read here today may surprise you...




  • Many people call Borrelia burgdorferi spirochetes Gram negative bacteria. However, Borrelia burgdorferi are not Gram-negative bacteria even if a Gram negative stain works on them:

    "Borrelia were thought to be Gram negative because of their double membrane structure, but genetic analysis places them - along with other spirochetes - into a separate eubacterial phylum. Ultrastructural molecular and biochemical studies have emphasized the wide taxonomic gap between spirochetes and Gram-negative bacteria."

    - From "The Genus Borrelia" by Melissa Caimano. Prokaryotes (2006) 7:235-293.
  • Unlike Leptospira and Brachyspira, spirochetes in the Borrelia and Treponema genera appear to have acquired Phenylalanyl-tRNA synthetase (PheRS)  genes from Archaea through horizontal gene transfer. [1] Borrelia and Treponema have Archaea genes.
  • Somewhere along the line, an ancient Spirochaeta relative picked up genes from Archaea's order, Thermococcales. Borrelia and Treponema have close affinities with Thermococcus and Pyrococcus (not depicted on tree).[1]
  •  The fascinating thing about this genetic relationship is that these genes come from organisms which are extremely thermophilic organisms. They are extremophiles - which means they can live in extreme environments. Thermophilic extremophiles thrive in hot environments such as volcanic vents and hot springs. That genes from extremophiles would end up in mesophilic organisms which thrive in lower temperatures - such as in mammalian and acarian hosts - seems surprising. The highest temperature Borrelia garinii can still grow in is around 41-42 C. That's not anywhere near the high temperatures in which one finds Archaean Thermococcales (often over 60 C, sometimes as high as 100 C).
  • This all does seem really weird. But the reason why it isn't too far fetched to see genes from extremely thermophilic organisms in moderately warm Borrelia and Treponema is more easily understood once you know more about the wide diversity found within the genus Spirochaeta in general. A number of Spirochaeta species live in extreme environments and not just in humans, animals, or ticks. For example:
    • S. halophila lives in a high salinity pond on the Sinai shore.[2]
    • S. thermophila lives in marine hot springs in New Zealand and Russia.[3]
    • S. americana lives in alkaline, hypersaline Mono Lake in California.[4]
Champagne PoolWai-O-Tapu, near Rotorua, New Zealand by Christian Mehlführer

  • When looking at a phylogenetic tree, Spirochaeta is at the base of the tree and Borrelia and Treponema branch off later. Based on this, the best assessment one can make about the gene transfer from Archaea to Spirochaeta is that the most recent common ancestor of Spirochaeta, Borrelia, and Treponema had to have been very similar to thermophilic Spirochaeta.
  • My running joke on this is to imagine a pile of thermophilic Archaea and thermophilic Spirochaeta hanging out around a hot spring together, laughing, joking, and flirting. Before you know it, horizontal gene transfer occurs, and a new form of spirochete is born. (This would make for a good Far Side comic, I just know it.)
  • As if having Borrelia acquire Archaea genes wasn't interesting enough, it's been thought that ProS prolyl-tRNA synthetase (BB402) was acquired from a eurkaryote.

  • Treponema spirochetes have a symbiotic relationship with termites. These spirochetes help termites in breaking down cellulose in wood in the termites' guts. So it isn't just ticks which have a symbiotic relationship with spirochetes - termites have one, too.[1, 5]

  • Borrelia burgdorferi survives on the equivalent of tick antifreeze in the tick's midgut inbetween tick blood feeding cycles. Borrelia burgdorferi prefers glucose when in the tick, but it will feast on glycerol instead. See: http://spirochetesunwound.blogspot.com/2011/10/lyme-disease-spirochete-feasts-on-tick.html
  • Both Borrelia hermsii and Borrelia burgdorferi metabolize chitobiose and N acetyl-glucosamine, a nutrient of these spirochetes and the major constituent of chitin for the exoskeletons of ticks.[6]
  • Borrelia have most of the genes required for the enzymes which make up the mevalonate pathway - a metabolic pathway used by the bacteria for synthesis of isoprenoid precursors. Isoprenoids are very important compounds which are found in over 30,000 products from the three domains of life (Eukaryotes, Prokaryotes, and Archaea). One interesting proposal about how Borrelia has the genes required for these enzymes for this pathway is that they come from the genetic cenancestor - an ancestor which predates the split into the three domains.[7]
     
  • In Act II of Samuel Beckett's play, Waiting For Godot, one character, Estragon, curses at the other, Vladimir, by calling him, "Gonococcus! Spirochete!"
Spirochetes continue to hold surprises and mysteries for us all... both good and bad. Another interesting installment of strange spirochete facts could be posted here - probably not too far in the future.

References:

1) Cheryl P Andam and J Peter Gogarten. Biased gene transfer and its implications for the concept of lineage. Biology Direct 2011, 6:47 doi:10.1186/1745-6150-6-47
2) Greenberg EP, Canale-Parola E: Spirochaeta halophila sp. n., a facultative anaerobe from a high-salinity pond. Arch Microbiol 1976, 110:185-19
3) Aksenova H, Rainey F, Janssen P, Zavarzin G, Morgan H: Spirochaeta thermophila sp. nov., an obligately anaerobic, polysaccharolytic, extremely thermophilic bacterium. Int J Syst Bacteriol 1992, 42:175-177
4) Hoover RB, Pikuta EV, Bej AK, Marsic D, Whitman WB, Tang J, Krader P: Spirochaeta americana sp. nov., a new haloalkaliphilic, obligately anaerobic spirochaete isolated from soda Mono Lake in California. Int J Syst Evol Microbiol 2003, 53:815-821.
5) Droge S, Frohlich J, Radek R, Konig H: Spirochaeta coccoides sp. nov., a novel coccoid spirochete from the hindgut of the termite Neotermes castaneus. Appl Environ Microbiol 2006, 72:392-397.
6) Tilly, K., Elias, A.F., Errett, J., Fischer, E., Iyer, R., Schwartz, I., et al. Genetics and regulation of chitobiose utilization in Borrelia burgdorferi. J Bacteriol 183: 5544–5553.
7) Jonathan Lombard and David Moreira. Origins and Early Evolution of the Mevalonate Pathway of Isoprenoid Biosynthesis in the Three Domains of Life. Mol Biol Evol  2011, 28 (1): 87-99. doi: 10.1093/molbev/msq177 http://mbe.oxfordjournals.org/content/28/1/87.full


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Wednesday, February 29, 2012

0 A Win For Free Access To Publicly Funded Research

A couple weeks ago I posted about the Research Works Act, and how it would force the public to pay twice for research their hard earned tax dollars already funded.

Today, I'm glad to report that the Research Works Act was rejected. Representatives Issa and Maloney pledged not to move the legislation forward. Infojustice's web site posted about this turn of events, and scathing commentary has ensued concerning the pay wall that is Elsevier.

Read about it here: http://infojustice.org/archives/8477

Also, see this article in The Scientisthttp://the-scientist.com/2012/02/28/elsevier-abandons-anti-open-access-bill/


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Sunday, January 22, 2012

0 US HR Bill 3699 Would Put Tax Payer Funded Science Behind Pay Walls

US HR Bill 3699: I have a stake in this one. Many people have a stake in this one. I think that tax payer funded scientific research should be open access and published online as it has been in PLoS ONE and PubMed.

I value high quality peer-reviewed research. It's important. And peer-reviewed journals with high standards and ethics are necessary.

Given the amount of work involved, I think it's okay for privately funded research to be behind a pay wall for certain period of time - publishers need to recoup their money for editing and publishing journals which include not only research papers but articles, letters, and reviews.

Once more knowledge milestones are met and that privately funded research becomes effectively dated then it would best be released into the wild where the general public and students at community colleges and high schools could access it for free.

But this bill? This bill would ensure charging access to tax payer funded research.

An excerpt from the Doing Good Science blog on Scientific American web site pretty much sums up my own thoughts about it:
"The public is all too willing already to see public money spent funding scientific research as money wasted. If members of the public have to pay again to access research their tax dollars already paid for, they are likely to be peeved. They would not be wrong to feel like the scientific community had weaseled out of fulfilling its obligation to share the knowledge it builds for the good of the public. (Neither would they be wrong to feel like their government had fallen down on an ethical obligation to the public here, but whose expectations of their government aren’t painfully low at the moment?) A rightfully angry public could mean less public funding for scientific research — which means that there are pragmatic, as well as ethical, reasons for scientists to oppose the Research Works Act."
Read more commentary about this at the Doing Good Science blog on the Scientific American web site:
http://blogs.scientificamerican.com/doing-good-science/2012/01/06/the-research-works-act-asking-the-public-to-pay-twice-for-scientific-knowledge/

The original text of US HR Bill 3699:
http://thomas.loc.gov/cgi-bin/query/z?c112:H.R.3699:


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Tuesday, November 8, 2011

0 Two Notable Antibiotic Articles - Long-term Effects & Alternatives

H. pylori: Friend or foe?
Answer: It depends...
I know some of you reading along may have already seen this, but I think it bears mentioning again and also bears mentioning for those who may not have seen it: The New York Times recently published an article on the long-term effects of antibiotic usage, "In Some Cases, Even Bad Bacteria May Be Good".

After reading the above link, I found it fascinating and disturbing that antibiotics not only could contribute to obesity - the hypothesis originally being test driven by the writer - but that antibiotic use could also lead to allergies, inflammatory bowel disease, asthma, and gastroesophageal reflux. These are conditions which are not only common in Lyme disease patients, but in the general population as well.

Among the astonishing findings in this article:
  • Eradicating H. pylori infections entirely leads to the inability of ghrelin (a hunger hormone secreted in the stomach) to decrease in the stomach, thus leaving the brain to think it's always time to eat more. Therefore, lack of infection = eating more = weight gain.
  • Researchers found that the ratios of various bacteria in the guts of obese mice and obese humans were significantly different from those of lean controls, suggesting that altering the stomach’s microbial balance with antibiotics might put patients at risk for gaining weight. H. pylori is not the only culprit for change.
  • Less H. pylori in someone's system is associated with a greater risk of not only asthma but gastric reflux disease as well.
  • The human body contains a very complex bacterial ecosystem which we don't know anywhere near as much about as we should. Knowing about it is important in understanding the cause for disease and how to prevent it.
  • It's not just antibiotics that are changing the human microbiota - many aspects of modern life, including diet, smaller families, more hygienic practices and improved public sanitation, are affecting our bacterial communities.
The research cited contains sobering news and adds to the realization that as much as antibiotics have brought deadly infections under control and saved lives, they can have negative side effects and possibly more longer term consequences than at first realized.

All this said, I have been an advocate of antibiotic usage to treat Lyme disease - especially in its early stage and with a clear case of neuroborreliosis - because antibiotics have been tested and used in clinical trials for many years for their effectiveness. It's  important in the case of neuroborreliosis to ensure that treatment can pass the blood-brain barrier, and so far antibiotics have been tested which are demonstrated to have this property.

So I still stand by the use of antibiotics for their effectiveness and documented record for helping patients everywhere. However,  I am aware that in the future, antibiotics may not work as well as they once did due to antibiotic resistance, and this knowledge of longer term effects concerns me as well. Alternatives will need to be found that are safe and effective.

What sort of treatment could be available other than antimicrobial herbs?

The answer may be as close as your local wallaby.

Okay, well, for most people reading this, wallabies are hardly local to them - unless you are one of my Australian readers or you have a decent zoo nearby.

Last month, Byte Size Biology blog published an entry on the innate immune system and research on cathelicidins, specifically those peptides found within marsupials - including wallabies - which can fight off infection.

A baby kangaroo (joey) or wallaby is born in its fetal stage and must travel across its mother's abdomen and into a pouch to complete development. This can expose the fragile fetus to all sorts of germs, so what protects it? While the joey has adaptive immunity which is quite undeveloped, it can produce some killer all-purpose peptides he can use against microbes.

The same class of peptides are produced in Kanga’s milk. (Think of the idea as being similar to colostrum in cows, perhaps?) Collectively they are known as cathelicidins. Only about 30 amino acids long, these highly charged molecules kill both gram-positive and gram-negative bacteria.

Preliminary studies were conducted on the use of cathelicidins as antibiotics. The author of Byte Size Biology wrote:
"They used cathelicidins from wallaby and platypus to kill human pathogens: P. aeruginosa, K. pneumoniae and A. baumanii, including antibiotic resistant strains. Cathelicidins were much more effective than, well, antibiotics against those bacteria. Also, cathelicidins did not kill human red blood cells, which makes them a potential drug. Of course, immune reaction against cathelicidins as a foreign still needs to be checked, among many, many other things, but the whole idea of looking at marsupials is that, as mammals, they may be able to supply us with clues on how to synthesize a cathelicidin to be used as a drug in humans."
More research is needed, obviously, but this may be one option to antibiotics sitting in your medicine cabinet of the future.

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Tuesday, October 25, 2011

0 Stony Brook Young Investigators Series On Lyme Disease

Ixodus ticks that carry B.burgdorferi.
Photo Credit: http://www.freewebs.com/
lymeandautism/GF-596-4ticks_cm.jpg
Stony Brook University has an online journal of science called The Young Investigators where students from the school write an in-depth article with citations on different topics.

Nadya Peresleni, Editor in Chief of the journal and undergraduate class of 2011, wrote a report on Lyme disease that I think is pretty good - it's detailed, touches upon the controversy over treatment in a matter-of-fact manner, describes the immunological and inflammatory aspects of the infection, and leaves some ideas about areas to target for future treatment options.

I found this paragraph to be of interest, and there is much more in the article that is good to read:
"Along with Dr. Benach's work, the laboratory of Professor Martha B. Furie has published on the role of interferon-gamma (IFN-γ), a cell-signaling molecule of the immune system, in the endothelial tissue of a genetically engineered mouse model that was infected with B. burgdorferi. 
"IFN-γ is like a molecular switch that turns on chronic inflammation," explained Dr. Furie. When the bacteria disseminate throughout the body after the tick bite, they activate the endothelium and begin the inflammatory process by attracting T lymphocytes that secrete IFN-γ [22]. The inflammation was found to be due, in large part, to a synergistic effect of B. burgdorferi and IFN-γ, which together activate the transcription of a series of genes in endothelial cells. These genes encode chemokines, or chemoattractants, specific for T lymphocytes. 
Interestingly, there seemed to be selection for those T lymphocytes that secreted more IFN-γ, and the result was a positive feedback loop that generated more and more IFN-γ, leading to a state of chronic inflammation in the tissue. The damage to human tissues is likely caused by the body's reaction to the bacteria, not the bacteria themselves [22]."

Yes, but the question remains as to whether the damage left behind is causing symptoms - or if the inflammation is caused by bacteria which are still viable is part of the problem... Or both.

This article mentions persistent infection and offers citations to examples - and it also mentions the above kind of mechanism for producing symptoms.

Check out the entire article here: http://www.younginvestigators.com/article-lyme-disease-overview.php


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Tuesday, September 27, 2011

1 LDA-Columbia Lyme 2011 Conference Line-up

On October 1 and 2, there will be a combined LDA/Columbia-Lyme Conference held in Philadelphia, Pennsylvania.

Below is an outline of the conference speakers and topics...

Keynote Speaker: J. William Costerton, PhD
The Role of Biofilms in Chronic Bacterial Infections

Eva Sapi, PhD
Killing Borrelia: An impossible job?

Jason A. Carlyon, PhD
Interior Decorating: Anaplasma phagocytophilum Remodels Its Host Cell-Derived Vacuole into A Protective Niche

Richard Marconi, PhD, Co-Course Director
c-di-GMP Regulates Key Steps in the Enzootic Cycle of Tick-Borne Spirochetes

Chris Earnhart, PhD
Lyme disease vaccine: an update on recent progress

Dr. Ed Masters Memorial Lecture: Robert S. Lane, PhD
Diversity of Borrelia burgdorferi s.l. genospecies and genotypes in California, and Implications for human infection.

M. Karen Newell Rogers, PhD
A New Model of Intervention for Lyme Disease by Targeting Chronic Inflammation and Selective Aspects of Immune Activation

Robert Yolken, MD
Infections and Human Neuropsychiatric Diseases

Josep Dalmau, MD, PhD
Clinical spectrum and cellular mechanisms of autoimmunity to NMDA and other synaptic receptors

Dr. John Drulle Memorial Lecture: John Aucott, MD
Early microbiologic and immunologic events in Lyme disease

Reinhard K. Straubinger, PhD
Canine and equine Lyme borreliosis – The animals’ perspective of the disease.

Benjamin J. Luft, MD
Diagnostics: update on protein arrays and new Lyme assays

Brian Fallon, MD, Co-Course Director
What is Chronic Lyme Disease? Models and evidence

Andrew W. Walter, MD
Update on Ehrlichiosis and Hemophagocytic Lymphohistiocytosis in Children

Andrea Gaito, MD
Clinical Evaluation and treatment of Lyme Arthritis; An autoimmune perspective

Ingeborg Dziedzic, MD
What everyone should know about Eyes & Lyme Disease

Vijay Thadani, MD
Epilepsy update: Distinguishing Epileptic from Non-epileptic seizures

Steve Bock, MD
Complementary and Integrative Medical approaches to Chronic Tick-borne Disease

Elizabeth Maloney, MD
The treatment of Lyme disease - a critical review of the literature – lessons, gaps, and future research needs



I think this conference holds more scientific weight to it than other Lyme disease-related conferences I've seen, so if anyone is going to be in Philly and attends, please take notes to share with us all.

(I won't be able to attend as I have a previous commitment scheduled before I knew this conference was going to be held at this time in October.)

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Friday, April 29, 2011

4 Top 10 Tips For Doing Your Own Lyme Disease Research

Here are my top 10 tips to share for doing your own Lyme disease research. Pretty simple and straightforward - and if you have any to add, please share in comments below.

1) Use the scientific, Latin terms for everything. You can use common terms, too, but Latin will give you more results and more specific results.

Examples:

Instead of "Lyme disease" use "Borreliosis".
Instead of "Neuro Lyme" use "neuroborreliosis".
Instead of "Lyme bacteria" or "infection" use "Borrelia burgdorferi".

2) Find out which terms microbiologists and scientific researchers use in their own papers and classes and then apply them to your search.

Examples:

Instead of "coinfection" use "polymicrobialism" or "polymicrobial".
Instead of "can't think straight" use "cognitive symptoms".
Instead of "spinal tap" use "lumbar puncture".
Instead of "shooting and burning pains" use "paresthesia".
Etc. - you get the idea.

Look at online and offline medical dictionaries for words that describe your symptoms and plug those into a search engine.

3)  Move your search away from general Google search to Google Scholar. You can get specific results for only scientific papers and patents that way.


4) Whenever you don't understand a term, use Wikipedia for an explanation.

I add a note of caution here: Wikipedia is not always right, though it usually is correct on basic science definitions.

If you aren't sure, double-check by doing a more general search and rely on college and university web sites for definitions. You may want to restrict your domain search to .edu web sites.

5)  Read educational institution web sites in general.

You may be surprised to find out what research is being done now on Lyme disease and coinfections which hasn't been published yet. Bookmark these items and check PubMed for the university name and researcher(s) name(s) periodically, as a paper will eventually be published.

6) Passively collect research information on your own web site or inbox by using RSS feeds.

If you look at the right column of this page and scroll down, you will see a number of Lyme disease and other disease-related and alternative medicine articles that are directly getting posted to this site all the time.

You can do the same with your own web site - or if you don't have a web site - by using an RSS reader or by subscribing to an RSS feed that gets sent to your email address.

This way, research comes to you and you don't have to always go do a search for it.

7) Look at major professional organizations' web sites - even if you may not agree with everything said - at least you will know what's going on.

Read the IDSA's web site periodically and be aware of how they view the issues around Lyme disease and infectious diseases in general. See what the NIH, CDC, and organizations have to say, and even more, dig deeper and look at what people from those organizations say in their research on PubMed and other online publication hubs. Some of what you find may surprise you.

8) Look at major online science web sites geared towards  a more general audience  (not specifically written for professionals) periodically.

Science Daily is a good example of this, and if you look at the bottom of each article, you will often see a link to the original paper or source on which they based their article. Check out the original source for more information - often it leads to finding out about other research the same researchers did on Lyme disease and coinfections.

Also, use the search function in Science Daily to look up terms such as "Lyme disease", "Borrelia", "Babesia" and even "Malaria". You may find interesting articles and older research from their archives this way.

9) Buy microbiology, acarology, and entomology text books for cheap and used at college bookstores which are trying to get rid of all old textbooks, "fire sales",  Amazon.com, and independent used bookstores near you.

While these textbooks can be dated, you might find information in them that could be useful and give you ideas of where to search next. Note that a lot of the basic information on Lyme Borrelia hasn't changed - but there has been a more refined and detailed understanding of what Borrelia is about over time, though, and those details need to be picked up by reading more recently published papers and books. (I say this, stating that a lot of Lyme disease research I see being cited online for and by patients is a bit outdated - we need to update these sites to reflect the state of the science.)

(You can also see if any friends or relatives have some lying around they're willing to lend or give to you.)

10) Search various libraries online, and participate in your local interlibrary loan program.

Can't afford that $500. book on microbiology? See if you can borrow it through your library's interlibrary loan program.

You will usually have a shorter time limit on borrowing books that are in high demand - some books have to be returned in a week. So if you need more time to work on it, ask someone to copy select passages for you from it to make notes on them later after you return the book.

Also, in many areas you can sign up for a program that will allow others to pick up books for you at the library on your behalf if you are housebound and too ill to go out - see if your area has one and sign up if you need it. This is good program to use in general for any material you may want to borrow for your own personal use.

And a bonus, Number 11:

Have a family member, friend, or friend of a friend who is already studying clinical microbiology, molecular biology, and/or genetics (immunology is helpful, too) help you decipher what you don't understand - and to tell you whether or not they think the findings are significant and which questions are not answered by a particular study that would be useful to have answered.

This may be a tricker bit, because not everyone is going to either have the time to respond to your request for help on this or hold the belief that your research is not worth the effort because they may believe that Lyme disease cannot persist and you are wasting your time.

Unfortunately, this is the truth of it - but in the true spirit of scientific inquiry and basically being stubborn, some people may be willing to help you at least a little bit.

My advice here is the less well-known the person is to you, the better it is to keep personal details out of the query. Also, keep your email or discussion brief, polite, and to the point while avoiding discussing the controversy. This is not to invalidate or dismiss your experience - but being said out of practicality and diplomacy: Busy people are more likely to respond to something in an unbiased fashion if you keep it simple and short.

Happy researching!

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Wednesday, April 20, 2011

34 News: Institute of Medicine Releases Lyme Disease Workshop Summaries

Source link: http://www.iom.edu/Reports/2011/Critical-Needs-and-Gaps-in-Understanding-Prevention-Amelioration-and-Resolution-of-Lyme-and-Other-Tick-Borne-Diseases.aspx?utm_medium=etmail&utm_source=Institute+of+Medicine&utm_campaign=04.20.11+Report+-+Lyme+Disease+%26+Other+Tick-Borne+Diseases&utm_content=New+Reports&utm_term=Media

To read the Workshop Summaries, click on the link at the top and look in the righthand column - you'll see gray buttons that say "Download Report" or "Read Report Online For Free". If you want to download a pdf of the report, you'll need to supply your email address and other info. If you just want to view it online, click "Read Report Online For Free" and there will be no request for personal information.

Once you select "Read Report Online For Free", by the way, you have an opportunity to download a 21 page summary of the report (direct download) by clicking on a link for it on the lefthand column. Otherwise, the full report is 468 pages long.

[CO update: The 21 page summary gives the barest of outlines of what was discussed, along with a list of those who attended - you are much better off reading the 468 page report.]

One thing to note here is that this appears to be a report on what was discussed at the Institute of Medicine (IOM) workshop on tickborne diseases in October 2010 and not a final position piece stating the IOM's consensus on how Lyme disease and tickborne infections should be approached through research, prevention, or treatment.
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Thursday, April 14, 2011

13 Books: Borrelia. Plus a lesson in terminology.

Borrelia: Molecular Biology, Host Interaction and Pathogenesis. If you have GB £159 or US $310 on hand, and you want to know the state of the science on Borrelia including Borrelia burgdorferi, afzelii, garinii, and its relapsing fever relatives - this is a good book to get.

If you would prefer to review the book before purchasing - or don't want to purchase it at all - check out your local library's interlibrary loan program.


See a detailed chapter outline at this link: http://www.horizonpress.com/borrelia

I have yet to do a review on this book as it is information dense and takes some time to read through - but I pulled some highlights from the chapter outlines (it is pretty robust for an outline, I have to admit)  and provided some vocabulary translation in which some readers may take an interest:
"B. burgdorferi strain B31, the B. burgdorferi type strain, has been studied in the most detail and harbors twelve linear and nine circular plasmids that comprise about 612 kbp. The plasmids are unusual, as compared to most bacterial plasmids, in that they contain many paralogous sequences, a large number of pseudogenes and, in some cases, essential genes. In addition, a number of the plasmids have features suggesting that they are prophages. Some correlations between genome content and pathogenicity have been deduced and comparative whole genome analyses promise future progress in this arena. [CO comment: Refer to Ben Luft's and Steven Norris' research on Bb strains and their ability to cause infection in human hosts.]"
In general, the whole plasmid thing is just weird. Having plasmids that take up one third of your genome is interesting.

Circular plasmids? No problem. You find them in bacteria all the time.

Linear plasmids? That is a bit unusual. Linear plasmids used to be thought of as only in eukaryotic organisms - organisms with a cell nucleus - not prokaryotic organisms like bacteria. Linear plasmids are also found in viruses. But they are found in few bacteria - Borrelia burgdorferi being one of them.

But prophages...  These are very interesting, and what makes some Borrelia strains more harmful to their hosts. That viral genes end up in Borrelia plasmids is pretty fascinating to me, even though this sort of thing happens with other bacteria too - it's fascinating and adds to Borrelia's existing complexity.

Translation for biology/genetics beginners:

(You might want to check this out sometime: http://en.wikipedia.org/wiki/Introduction_to_genetics .)

chromosome = A chromosome is an organized structure of DNA and protein that is found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences.

plasmid  = Usually described as a double-stranded unit of DNA that replicates within a cell independently of the chromosomal DNA. Three of the plasmids found in all Borrelia burgdorferi isolates have been described as "mini-chromosomes".

Your handy little Bb plasmid cheat sheet:
cp = circular plasmid
lp = linear plasmid
cp26 = needed for viability, encodes OspC.
lp25 and lp28-1 = needed for infectivity in mice; lp28-1 involved in antigenic variation.
cp32 = contains prophage material; encodes a BpaB protein, which appears to play a role in replication and segregation.
lp54 = encodes OspA/B operon and decorin-binding protein operon dpbBA

Other Borrelia plasmids (relapsing fever):
cp32 = described in B. hermsii; does not contain an OspE/F/Elp lipoprotein (unlike Bb)

Plasmids make up about a third of Borrelia burgdorferi's entire genome. (Fraser et al, 1997; Casiens et al, 2000). Linear plasmids are the most genetically diverse part of Bb's genome, and rearrangements and deletions inside them contribute to their uniqueness.

In Bb, there is a division of labor between the chromosome and extrachromosomal elements or “plasmids”. Genes encoded on the chromosome tend to do housekeeping - housekeeping genes are present in single copy - while genes on the plasmids tend to be Borrelia-specific, of unknown function or involved in the infective cycle, and present in multiple, related copies.

Source material:
The Prokaryotes: A Handbook on the Biology of Bacteria (Vol. 7) by Martin Dworkin and Stanley Falkow.
The Linear Hairpin Replicons of Borrelia burgdorferi. Kerri Kobryn. Microbiol Monogr (7) Universite de Sherbooke, Sherbrooke, QC, Canada

genome = the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA.

pseudogene = dysfunctional relatives of known genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Also known as mutationally damaged or "Junk DNA" - it is not always necessarily "junk" - its function is simply unknown at this time.

essential gene = genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell - if they don't work, the organism dies.

paralogous = This one takes a little more explaining...

Homologous gene sequences = the same, where "homo" means "like, similar" and "hetero" means "different, divergent".

For example, in general, if two or more genes have highly similar DNA sequences, it is likely that they are homologous. "Paralogous" means they are homologous gene sequences which are similar but they occupy different positions or locations in the same genome.

Sequence similarity is often seen in organisms that evolved from the same common ancestor. However, sequence similarity may also arise without common ancestry - short sequences may be similar by chance, and sequences may be similar because both were selected to bind to a particular protein, such as a transcription factor. Such sequences are similar but not homologous.

prophage = Okay... This is where things get weird. A prophage is a phage (viral) genome inserted as part of the linear structure of the DNA chromosome of a bacterium. A temperate phage is integrated into the host chromosome or existing as an extrachromosomal plasmid. This is a latent form of a bacteriophage, in which the viral genes are incorporated into the bacterial chromosomes without causing disruption of the bacterial cell.

In other words, a bacteriophage is a virus that lives inside bacteria, and a prophage is viral genetic material that becomes part of the chromosome in the bacteria (see virus to left, injecting its genetic material inside a non-spirochetal bacteria). So, in this case, at some point in time, a phage known as phiBB-1 (also spelled φBB-1) made its viral genes part of Borrelia burgdorferi's plasmids.

In prophages in general, if the host bacteria is damaged, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the lytic cycle.

Prophages are important agents of horizontal gene transfer, and are considered part of the mobilome.

In many bacterial species, prophages figure prominently in the biology of these cells, often conferring key phenotypes that can convert a non-pathogenic strain into a pathogen. In other words, while it's residing inside the bacteria, the prophage can turn bacteria that is harmless into harmful bacteria.

Such phenotypic changes can include prophage-encoded toxins, bacterial cell surface alterations, or resistance to the human immune system.

Prophage integration into the host genome can inactivate or alter the expression of host genes. In addition to these direct genetic alterations associated with the addition or inactivation of genes, prophages can also alter the phenotype of bacteria at the population level by facilitating the spread of favorable genes through transduction. (transduction = the process by which DNA is transferred from one bacterium to another by a virus.)

Its significance in Borrelia burgdorferi:

It's not discussed much on Lyme disease patient forums, but some strains of Borrelia burgdorferi have had their plasmids invaded by prophages. The presence of those phages - their viral genetic material - can make Borrelia burgdorferi more pathogenic.

phage particles in Borrelia burgdorferi
from Eggers et al
The phiBB-1 prophage is capable of transducing a cp32 between cells of the same isolate and between different Bb isolates. This means this prophage could play a role in the genetic diversity of different Bb isolates.

The structural proteins for phiBB-1 have not yet been identified, and a number of proteins encoded on cp32 have no homologs in any databases outside of Bb.

cp32 expresses a few outer surface or membrane proteins, of which ospE is the only one of which its function is known. It binds to complement factor H and helps Bb evade the complement system of the host.

A number of different bacteriophages have been observed in association with spirochetes and are being researched now. It may contribute to Lyme disease's ability to persist.

Well-known research on this includes this study:
Eggers et al http://www.ncbi.nlm.nih.gov/pubmed/11466280

Source material:
Wikipedia: http://en.wikipedia.org/wiki/Prophage
Wikipedia: http://en.wikipedia.org/wiki/Introduction_to_genetics
Borrelia: Molecular Biology, Host Interaction and Pathogenesis.
The Prokaryotes: A Handbook on the Biology of Bacteria (Vol. 7) by Martin Dworkin and Stanley Falkow.

pathogenicity = the ability of a pathogen to create infectious disease in an organism.

One of the relevant points to be gleaned from the above is that the genetic makeup of the plasmids are related to the virulence and pathogenicity of Borrelia. (virulence = the degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host.)
"The highly unusual segmented genomes of Borrelia species can contain over 20 autonomously replicating DNA molecules. Many of the molecules, including the chromosome, are linear with covalently closed hairpin ends. Current knowledge of the replication and maintenance of DNA molecules will be reviewed, including the process of telomere resolution, whereby the covalently closed hairpin ends are generated from replicative intermediates. Finally, the proposal that reverse telomere resolution is the driving force shaping the ongoing rearrangements and telomere exchanges in the linear replicons of Borrelia species will be discussed."

Translation for biology/genetics beginners:

chromosome = A chromosome is an organized structure of DNA and protein that is found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences.

nucleotide = molecules that when joined together make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism.

covalently closed hairpin ends = strands of genetic material curve back on itself in a hairpin pattern.

telomere = a region of repetitive DNA at the end of a chromosome, which protects the end of the chromosome from deterioration. The telomere shortening mechanism normally limits cells to a fixed number of divisions, so a shorter telomere means there are fewer divisions left for that cell and it will die sooner. Animal studies suggest that this is responsible for aging on the cellular level and sets a limit on lifespans.

telomere resolution = when the replicated linear DNA ends are processed by DNA breakage followed by joining of DNA free ends to the complementary strand of the same DNA molecule.

reverse telomere resolution = when linear DNA cleaves (splits) and joins hairpin telomeres on unrelated (rather than related) DNA molecules. The new linked plasmid structure could fuse to another linear plasmid in the future, and this explains how Borrelia can engage in telomere exchanges. This process may play a major role in the development of weird linear plasmids in Borrelia and their ability to confuse the immune system.

replicon = a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication. For most prokaryotic chromosomes, the replicon is the entire chromosome.

This part, I think most readers will know about the last sentence - but suspect they will be less familiar with the first half:

Borrelia are not 
Gram-positive...  But... they are not exactly Gram-negative bacteria, either.
"Although Borrelia spirochetes are often, but mistakenly described as Gram-negative bacteria due to their diderm, i.e. double-membrane envelopes, a closer examination reveals significant differences in composition and architecture. Probably most striking is the lack of LPS, the presence of major surface lipoproteins at the host-pathogen interface during transmission, persistence and ensuing pathogenic processes and the additional function of periplasmic flagella in defining cell shape. While surface lipoproteins such as the Osps interact with a variety of ligands in different organ tissues, they are also targets of the immune response and several have emerged as vaccine candidates."
I found information confirming the fact that Borrelia is not Gram-negative or Gram-positive. It's its own special thing:

Borrelia were thought to be Gram negative because of their double membrane structure, but genetic analysis places them - along with other spirochetes - into a separate eubacterial phylum. Ultrastructural molecular and biochemical studies have emphasized the wide taxonomic gap between spirochetes and Gram-negative bacteria. ( The Genus Borrelia. Melissa Caimano. Prokaryotes (2006) 7:235-293.)

Translation for biology/genetics beginners:

Gram-negative = Gram-Negative Bacteria are simply called this because of their detection by the Gram’s Stain test in which they do not retain the crystal violet color (dye) in their cell wall. The Gram-Negative bacteria cell-wall holds the pink or reddish dye once a counterstain chemical is used. This is characteristic of bacteria that have a cell wall composed of a thin layer of a particular substance (called peptidoglycan).

diderm = double-membrane envelope consisting of an inner cytoplasmic membrane and outer membrane found in Gram-negative bacteria.



double-membrane envelopes = See the picture to the left. Monodermic bacteria (mono = one) have one membrane, and didermic bacteria have two (di = two) membranes - the inner membrance (cm) and outer membrane (om).


LPS
= Lipopolysaccharides (LPS), also known as lipoglycans, are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals. [CO comment - a question for my readers: If Borrelia burgdorferi do not have LPS, what is producing the endotoxins everyone in the Lyme patient community says are important to detox? Keep reading, the answer is downstream...]

lipid = Lipids are a broad group of naturally occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules. In this context, lipids make up the inner membrane of Borrelia burgdorferi.

polysaccharide = Polysaccharides are polymeric carbohydrate structures, formed of repeating units (either mono- or di-saccharides) joined together by glycosidic bonds. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.

lipoproteins = A lipoprotein is a biochemical assembly that contains both proteins and lipids water-bound to the proteins. Many enzymes, transporters, structural proteins, antigens, adhesins and toxins are lipoproteins.

(a) external side view of Borrelia burgdorferi spirochete,
(b)  head-on view of cross-section of Bb, and (c)
side view of cross-section of Bb's diderm membranes.  
periplasmic = The periplasmic space or periplasm is a space between the inner cytoplasmic membrane and external outer membrane of Gram-negative bacteria or the equivalent space outside the inner membrane of Gram-positive bacteria. It may constitute up to 40% of the total cell volume in Gram-negative species, and is drastically smaller in Gram-positive species.

flagella = A flagellum is a tail-like projection that protrudes from the cell body of certain prokaryotic and eukaryotic cells, and functions in locomotion. (Flagella is plural of flagellum.)

Osps = Outer surface proteins. The outer membrane of Borrelia burgdorferi is composed of various unique outer surface proteins (Osp) that have been characterized (OspA through OspF). The Osp proteins are lipoproteins anchored by N-terminally-attached fatty acid molecules to the membrane. They are presumed to play a role in virulence, transmission, or survival in the tick.

ligand = Any substance (e.g. hormone, drug, functional group, etc.) that binds specifically and reversibly to another chemical entity to form a larger complex.
"Several borrelial proteins have been implicated in adherence to host cell surface proteins and extracellular matrix components and are likely to be involved in the homing of Borrelia to histologic compartments within each tissue, penetration of blood vessels and adherence to and migration through endothelial cells and tissue strata at distant sites. Activation of plasmin on the bacterial surface and induction of host proteases are thought to facilitate dissemination and/or inflammation. Most tissue damage appears to result from host inflammatory reactions. Although the mechanisms are not entirely understood, induction of cytokine/chemokine expression by bacterial lipoproteins and the resulting recruitment and activation of lymphocytes, macrophages and granulocytes play a major role in both local histopathology and constitutional symptoms. Despite their relatively low densities in tissues, Borrelia cause neurologic, cardiovascular, arthritic and dermatologic manifestations during the disseminated and persistent stages of infection by mechanisms that remain largely a mystery. Immune evasion mechanisms, including the vls antigenic variation system, complement-regulator acquiring surface proteins (CRASPs), down-regulation of highly antigenic surface proteins (such as OspC) and invasion of protective niches, permit the survival of the pathogens for months to years following infection despite robust antibody and cellular responses."
Translation for biology/immunology/genetics beginners:

host cell surface proteins = proteins on the surface of the host's cell.

extracellular matrix = Any material produced by cells and secreted into the surrounding medium, but usually applied to the noncellular portion of animal tissues. In other words - the space around the outside of cells, but not within cells.

histologic = related to cells and tissue on the microscopic level.

endothelial cells = cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.

plasmin = an enzyme present in blood that breaks down many blood plasma proteins, most notably, it breaks down fibrin clots (blood clots).

protease = an enzyme that breaks down proteins.

cytokine = small cell-signaling protein molecules that are secreted by the glial cells of the nervous system and by numerous cells of the immune system and are a category of signaling molecules used extensively in intercellular communication.

The term "cytokine" has been used to refer to the immunomodulating agents, such as interleukins and interferons. Biochemists disagree as to which molecules should be termed cytokines and which hormones. As we learn more about each, anatomic and structural distinctions between the two are fading.

chemokine = are a family of small cytokines, or proteins secreted by cells. Their name is derived from their ability to induce directed chemotaxis in nearby responsive cells; they are chemotactic cytokines. Chemotaxis is simply the act of cells changing their movement according to certain chemicals in their environment.

lymphocyte = White blood cells. Large lymphocytes include natural killer cells (NK cells). Small lymphocytes consist of T cells and B cells.

macrophage = white blood cells which phagocytose (engulf and then digest) cellular debris and pathogens, either as stationary or as mobile cells. They also stimulate lymphocytes and other immune cells to respond to pathogens.

granulocyte = a category of white blood cells characterized by the presence of granules (meaning "grains") in their cytoplasm (inside the cell membrane). These are thought of as the "phil" brothers of white blood cells: neutrophils, eosinophils, and basophils.

histopathology = the microscopic examination of tissue in order to study the manifestations or signs of disease.

vls = Gene locus in Borrelia burgdorferi which is required for encoding variable surface proteins.

vlsE = VlsE is a lipid-protein conjugate, found on the cell's outer surface during all Borrelia life stages. It is similar to a lipoprotein of the organism that causes African sleeping sickness. Unlike most proteins, VlsE is produced in many forms. It is a complicated protein with several variable regions (VRs), and six invariable regions (IRs).

When synthesizing VlsE, Borrelia periodically replace the VRs with new sequences. This replacement presents fresh surface antigens, and helps Borrelia remain invisible to the immune system. Within four days of being transferred to a mammalian host, VlsE will be produced with more than one VR suite, reducing the strength of the immune response. In ticks, VlsE does not modify the VRs. (Credit to Dr. Albert Burchsted, retired Field Biologist, for this description.)

antigenic variation = the mechanism in which an infectious organism alters its surface proteins in order to evade a host immune response. This change in antigenic profile may occur as the pathogen passes through a host population (also called "antigenic diversity") or may take place in the originally infected host.

The strategy is particularly important for organisms that a.) target long-lived hosts, b.) repeatedly infect a single host, and c.) are easily transmitted. Pathogens that express these characteristics and undergo antigenic variation have a selective advantage over their more genetically stable counterparts.

A number of bacteria use antigenic variation to evade the immune system, but Borrelia burgdorferi's method of antigenic variation is very complex and unusual compared to these.

In the case of Borrelia burgdorferi, the lp28-1 plasmid has been responsible for antigenic variation in vls locus - responsible for vlsE and the changing of Borrelia's outer surface proteins which helps it evade the immune system.

During the past decade, it was thought that removing the lp28-1 plasmid or altering its genetic material would remove Borrelia's infectivity entirely. It reduced it, but removing specific genes near the vlsE locus has done more to reduce Borrelia burgdorferi's infectivity.

The mutation of either of the genes encoding the two subunits of the RuvAB branch migrase blocked transfer of genetic information into vlsE during mouse infections, identifying the first required function for antigenic variation in the Lyme disease spirochete.

But basically, both the cis arrangement of vlsE and the vls silent cassettes in lp28-1 facilitate vlsE gene conversion.

See:
http://www.ncbi.nlm.nih.gov/pubmed/15501789
http://www.ncbi.nlm.nih.gov/pubmed/19266024
http://www.ncbi.nlm.nih.gov/pubmed/19997508

Source material:
The Linear Hairpin Replicons of Borrelia burgdorferi. Kerri Kobryn. Microbiol Monogr (7) Universite de Sherbooke, Sherbrooke, QC, Canada
Borrelia: Molecular Biology, Host Interaction and Pathogenesis.

complement = a small protein which mediates antibody response in the host's body. This is part of a complex immune system known as the complement system.

CRASPS = Borrelia produces complement regulator-acquiring surface proteins (CRASPs) that bind host complement factor H protein. Factor H protein is a negative regulator of the complement cascade (inactivates C3b). Borrelia produces a whole family of CRASP proteins. Different family members are able to interact with different factor H proteins from divergent hosts.

If that sounds too confusing, the thing to remember is that Borrelia has surface proteins which can bind to a host's complement's protein which then inactivates part of the complement system.

down-regulation = the process by which a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external variable. (Up-regulation is the opposite process.)

So, as I've stated before - researchers do know that the infection can be persistent - the question and controversy has been over whether or not infection persists after one has antibiotic treatment. 

It's my opinion so far that it can persist - especially if one has neuroborreliosis and has been undertreated or untreated. Those who have been suffering from neuroborreliosis and reading this will say it definitely can persist, based on their experience. The question remains as to how one can know whether or not the infection has been eradicated. This is what needs to be known. 

Also, there is persisting, and then there is persisting... One of my nightmare scenarios has been that when the IDSA Lyme disease guidelines panel states that Lyme disease does not respond to long-term antibiotic treatments, what it really means that none of the antibiotics which exist today can effectively eradicate all of it and the immune system isn't always capable of mopping it up after antibiotic treatment.

This is why people began experimenting with a number of alternative treatments: in their experience and opinion, antibiotic treatment either failed to eradicate the infection or stop their symptoms - and sometimes the side effects or infection with C. difficile led to the decision to stop antibiotic treatment.

Onward...

Lyme Disease in Humans - from the last chapter in Borrelia:
"Lyme disease is a rapidly emerging tick-borne, complex, multi-system infectious disorder caused by the spirochetal bacterium Borrelia burgdorferi. The ailment, which affects adults and children alike, is widespread in the Northern Hemisphere and it continues to expand as humans encroach on the sylvatic habitat of the spirochete's mammalian reservoirs."

"Since first identified in the 1970s the incidence of Lyme disease has increased more than 30-fold and it is now considered the most prevalent arthropod-transmitted infection in both the United States and Europe."
This is why I say doctors should look at the possibility of ruling it in, more than ruling it out...
"B. burgdorferi is transmitted by ticks of the Ixodes ricinus complex, including I. scapularis, I. ricinus and I. persulcatus. In North America, B. burgdorferi sensu stricto is the only species proven to be pathogenic for humans [CO note: Relapsing fever Borrelia are pathogenic to humans too, and some species of Borrelia have yet to be determined for their pathogenicity in humans.]. In Europe, both B. afzelii and B. garinii are most commonly associated with human disease.

The spirochete's genomic features, as well as its unique molecular architecture, are considered to have a seminal role not only in how it is transmitted from ticks to humans, but also how it triggers immune responses in afflicted individuals. Inflammatory manifestations associated with the disease result from the host's innate and adaptive immune responses to the bacterium, rather than from toxigenic molecules, which borrelia cannot produce. Indeed, the deposition of spirochetes into human dermal tissue generates a local inflammatory response that becomes manifest as erythema migrans (EM), the hallmark skin lesion of Lyme disease in North America. In Europe, two additional dermatologic disorders, borrelial lymphocytoma and acrodermatitis chronicum atrophicans (ACA) are frequently associated with infection. EM is frequently accompanied by 'flu-like' symptoms, including myalgias, arthralgias and fever, which are generally believed to be cytokine-mediated in response to hematogenous spread of the bacterium. If treated appropriately, the prognosis is excellent; however, if untreated, patients may develop a wide range of inflammatory clinical manifestations, most commonly involving the central nervous system, joints and heart. Within days of treatment, the signs and symptoms associated with the disease typically begin to subside, although in some individuals a complete recovery can take several weeks or even months. A minority of treated patients may go on to develop a poorly defined fibromyalgia-like illness, which is not responsive to prolonged antimicrobial therapy. Below we integrate current knowledge regarding the ecological, epidemiological, microbiological and immunological facets of Lyme disease into a conceptual framework that sheds light on the disorder that healthcare providers encounter."

According to this, Borrelia burgdorferi does not produce toxigenic molecules, and most symptoms are believed to be cytokine-mediated in response to hematogenous spread of the bacterium. (hematogenous = originating in or spread by the blood). They are talking about all Borrelia there.

Hm. That's interesting. Does that mean that what people think is a Herxheimer reaction due to the release of toxins is actually something else, some other process?

I wanted to know what the deal is with this, so I looked it up... Huh, this was interesting:

Borrelia have abundant glycolipids but they do not have an endotoxin-like lipopolysaccharide. And the authors' running hypothesis is that the Herxheimer reaction is due to the action of lipoproteins on toll-like receptors (TLR2) in macrophages and other cells. Apparently, if you infuse antibodies that recognize TNFa (Tumor Necrosis Factor alpha) into someone who is infected with related Borrelia recurrentis before giving them penicillin, it reduced the severity of a Herxheimer reaction (Fekade et al, 1996 - full text at preceding link). When cytokine levels get quite high, this contributes to the reaction. (Borrelia, p. 339)

So, does this mean that detoxing is useless because there is no toxin to removeThe paper goes on to state that "...lipoproteins from two other spirochetes, B. burgdorferi and Treponema pallidum, induce the biosynthesis of tumor necrosis factor in murine macrophages."

So when patients are having a Herxheimer reaction, it is a reaction to the die-off induced by the immune system - not a reaction induced by a toxin.

Regarding the bit in the last section on persistence: Researchers are somewhat divided on this, and even as I write this, studies are published on the use of long-term antibiotic treatment for some of this minority of treated patients with persistent symptoms.

Dattwyler co-wrote this chapter along with Radolf, and one has to wonder if it would have been written somewhat differently and been left open to more uncertainty had Volkman or Barthold co-written it? Something to think about there.

At any rate...the running hypothesis is that infectivity of Borrelia species depends heavily on the evasion from the host response. And this evasion can be based on multiple mechanisms.

You've gotta just love the closing quote on the end of one chapter in the book...

Not.
“If our work with Borrelia has taught us one thing, it is to expect the unexpected. So we should not be surprised to discover that this phylogenetic ancient spirochaetal microorganism has developed several solutions of  its own and that it does not always conform to the dogmatic structure and function of the cell envelope of Gram-negative bacteria. We therefore anticipate a bright future with many challenges and unsolved mysteries for several generations of Borrelia researchers.”
Yeah. Right. Your science project is my life, man. I'm not looking at this as some professional subject of interest. My focus in this is different from yours. By a longshot, baby. By a longshot.
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Thursday, March 31, 2011

17 Video: Shortcuts To Learning Immunology

I realize I posted a 14 part mini-series on Immunology not long ago and know that could be a bit much to bite off at once in order to learn more about the immune system.

So I've been spending time looking for shortcuts - ways for readers to quickly get up to speed on some of the terms and processes used when discussing the immune system.

I figure videos usually are the best way to begin learning for many people - so I have been watching them on Youtube to decide what to post here.

Let me just say that as entertaining as some of them are, I wish more of them were factually correct or just had more educational content in them.

I love the idea of using battle scenes from The Lord of the Rings movies as an analogy for the immune system - some creative guy did this, and it was hilarious. But most of it had no mention of the immune system or how it worked, beyond "the good guys are these immune cells, and the orcs are the invading pathogens". And then there was the guy who went so far as to make a 1950's style documentary on angry macrophages, with retro props and a fake ad for Solomon cigarettes... this documentary compared pathogens to invading Communists.

Unique. Original. Points for style. And yet, next to no substance.

What could have been both an entertaining and educational clip ended up an abysmal failure. C'mon guys, you can do better.


Anyway, I found what I hope are some of the better videos on Youtube that you can watch to learn more about the immune system, and the material on the first one will help you advance to the next video. Also, each video reinforces what you've seen in an earlier one - it helps familiarize you with the terms and concepts used.

Let me know if you have any trouble following these. For those of you who are already more advanced students of immunology and have gotten past all of this, I will be posting more intermediate and advanced videos on the immune system later. (Those who have watched these basic and intermediate videos first will be able to move on to the advanced section, which will mention toll-like receptors and interleukins.)

If you are a more advanced student and already understand those, then I would like to encourage you to comment more here and perhaps start your own blog to let people know more about the science of the immune system and infectious diseases like Lyme disease.

Knowing more about the immune system opens the door to understanding research out there done by the IDSA guidelines panel, scientific researchers in microbiology and molecular biology outside of the IDSA panel, the statements LLMDs have made about Lyme disease and its treatment, and claims other Lyme patients have made online.

Okay, without further delay, here are four videos which may prove useful for beginners - each under 10 minutes:

Immunology Overview [Time: 4:42] - overview of basic parts and terms of the immune system


The Immune System [Time: 9:36] - Basic explanation of the immune system and how it works.

Immune System, Part 1 [Time: 7:59] - Barriers and Non-Specific Defenses
Note that this video is accompanied by this easy to view PDF:
http://www.kirkwood.edu/pdf/uploaded/695/immune_and_lymphatic2.pdf



The Immune Response (Garland Science) [Time: 1:43]


That should be good to get you started.

Note that each one has slightly different information about the immune system, but the core material is the same. Being exposed to this information in different ways over time makes it easier to learn.
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