Lyme disease, science, and society: Camp Other

Tuesday, April 19, 2011

0 Chart: Effectiveness of different alternative medicine ingredients

I found this link on alternative medicine online that you might find interesting:

LINK: A visualization based on the effectiveness of different alternative medicine supplements, spices, oils, and herbs

Each item represented there is based on PubMed and Cochrane reports on large human blind placebo-controlled studies only.

If you click on the bubbles, you'll be taken to abstracts which support the use of those particular alternative medicines for specific conditions.

Note these directions found at the bottom of the page before you go there:
"The higher a bubble, the greater the evidence for its effectiveness. But the supplements are only effective for the conditions listed inside the bubble. (Mouseover the bubble to see what I mean.) 
You might also see multiple bubbles for certain supplements. These is because some supplements affect a range of conditions, but the evidence quality varies from condition to condition. For example, there’s strong evidence that Green Tea is good for cholesterol levels. But evidence for its anti-cancer effects is conflicting. In these cases, we give a supplement another bubble."
The chart is Flash based, but there is a link to a non-Flash version there if you prefer that (iPhone users take heed.)
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Monday, April 18, 2011

0 Research And A Personal Story: Computer scientist researches own Lyme disease

Well, this has been posted elsewhere, but I just had to share it here, too:

Computer scientist researched her own condition, Lyme disease

Source link: http://www.post-gazette.com/pg/11101/1138165-114.stm

Read the above article, and see if you see yourself (or someone you care about) in this woman's shoes. (I know that I can relate to her own search for reliable medical information, that's for sure.)

After much research from many different medical sources, Ms. Mankoff decided to try long-term antibiotics. After 18 months of antibiotic use she could stop treatment and go on to write professional papers, work full time, and do research on how members of the Lyme patient community seek out information on Lyme disease diagnosis, treatment, and support.

There is mention in the Post-Gazette article above that the paper based on her research of the Lyme patient community will be presented at an upcoming conference on computer-human interaction, CHI 2011.

That paper is:

J. Mankoff, K. Kuksenok, J. A. Rode, S. Kiesler & K. Waldman, Competing online viewpoints and models of chronic illness. In Proceedings of CHI 2011. To Appear (Full Paper)

And here is a link to the FULL TEXT (no subscription required):

http://www.cs.cmu.edu/~assist/publications/11MankoffCHI.pdf

If anyone happens to be in the Vancouver area this May 6 and would like to attend the session, it will be from 4:00-5:20 pm. (A link to the conference appears at the bottom of this post.)

A description is as follows:

Session Chair: Julie Kientz (University of Washington)
Competing Online Viewpoints and Models of Chronic Illness - Paper

Session Chair: Julie Kientz (University of Washington)
Competing Online Viewpoints and Models of Chronic Illness - Paper
Jennifer Mankoff Carnegie Mellon University,
Kateryna Kuksenok University of Washington,
Sara Kiesler Carnegie Mellon,
Jennifer A. Rode Drexel University,
Kelly Waldman Duke

Abstract »

People with chronic health problems use online resources to understand and manage their condition, but many such resources can present competing and confusing viewpoints. We surveyed and interviewed with people experiencing prolonged symptoms after a Lyme disease diagnosis. We explore how competing viewpoints in online content affect participants’ understanding of their disease. Our results illustrate how chronically ill people search for information and support, and work to help others over time. Participant identity and beliefs about their illness evolved, and this led many to take on new roles, creating content and advising others who were sick. What we learned about online content creation suggests a need for designs that support this journey and engage with complex issues surrounding online health resources.


If you wish to attend CHI 2011 for only a day session on site, you must be warned that registration is steep:
http://chi2011.org/attending/registration.html

If you can't make it to Vancouver and pay for admission, consider sitting at home, reading the pdf of the paper above, and emailing Ms. Mankoff with comments and questions.

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Sunday, April 17, 2011

5 One way to treat Borrelia naturally?

Many Lyme disease patients have used antibiotics for treating Lyme disease and other tickborne coinfections. They have years of scientific study behind them and many reports of patient improvement come from doctors and specialists - patients have had a lot of success with them.

But sometimes antibiotic use leads to various side effects, digestive problems, and potentially, undesirable secondary infection with C. difficile. Using probiotics can often help with digestive problems and prevent C. difficile, but it is not guaranteed.

In some cases - due to allergies or intolerance of the side effects - patients have to stop antibiotic treatment. Because of this, patients have opted at some point in their treatment to stop taking antibiotics after a while and switch to alternative treatments such as herbs.

Whether a patient decides to use antibiotics or herbs, one thing on the horizon seems certain: Eventually antibiotic resistance will lead to more restrictive use of antibiotics, and antibiotic resistance may challenge patients' ability to treat some of their own infections.

However, there is one completely natural possibility that might treat Borrelia and some other tickborne infections in the future which is rarely mentioned in the west other than as a curiosity - yet everyone in the world is surrounded by this abundant and prosperous source of healing from nature all the time.

Much as there are different probiotic bacteria are found in yogurt and probiotic supplements that Lyme disease patients take -- there are viruses in our environment that are helpful to us.

A lot people think of a few things when they hear the word "virus": they think of H1N1 or the swine flu, colds, herpes, HIV, and meningitis, for a start. Not good things. But like the probiotic bacteria that we consume in yogurt all the time, viruses are also present in our environment - in our food, our soil, our drinking water, and our own digestive systems.

Like adding probiotic mixes to your yogurt, these helper viruses have been approved by the FDA to be sprayed on the surface of cheese across the US in order to prevent the development of the bacteria, Listeria monocytogenes, from causing serious disease in pregnant women,  immunocompromised people such as cancer patients, and those with immuno-deficiences. Thousands of people can be severely sickened by Listeria and in some cases even die. So the use of these viruses in food such as cheese is beneficial.

In addition to providing protection from harmful bacteria in food, these helpful viruses have also been used to help save baby calves from dying of diseases which cause severe diarrhea and prevent salmonella from colonizing chickens.

The method for treating these cases was find out which bacterial strains the animals were infected with in order to find the viruses which would eat them. Then use these viruses just as they are found in nature, with no genetic engineering required - put the viral material in pills, injections, or lotions in order to treat the infection.

So this leads one to wonder if this all-natural, non-GMO treatment which is low-cost compared to antibiotics and so abundant in nature can kill off bacterial infections in animals - why can't they kill off infections in people too?

Well, they can.

Watch the next two videos, paying special attention to the first video.


The first video is a 48 minute BBC documentary on the use of viruses to kill bacteria, also known as "bacteriophage therapy" in the former Soviet republic of Georgia, in the Eliava Institute of Tblisi.

Note that if the institute seems run down, filming was done after the collapse of the Soviet Union and the hospital just came out of a civil war - thus buildings had poor maintenance, but the technology to use bacteriophage therapy was in place and used. (After a period of economic instability and social problems - followed by the Rose Revolution - Georgia and Tblisi have been doing much better in the past several years.)

So this documentary is a little dated but general principles remain the same - it explains very well what bacteriophage therapy is and how it has been used in Europe for over 60 years through the 1990's (it continues to be used today - more on recent research using phages will be posted this week).

Youtube (3 parts)

BBC Horizon - 1997 - The Virus That Cures


This second video is from Canadian television as well as CBS news and is more recent - it contains two clips back to back about two people who were treated with phage therapy and their results. Don't miss it - the results are amazing when you realize the initial prognosis each patient was given.

Case studies on phage treatment plus Evergreen College, 
Washington State phage research - [Time: 9:26 minutes]

Is bacteriophage therapy this effective? Does it have any pitfalls? Why don't we hear more about it here yet, given the rising number of cases of antibiotic resistance to deadly bacteria such as MRSA? What can it treat so far? How can this treatment help Lyme disease patients in the future? Here's just one more video just to get a different angle on it from Australian news (Channel 7 and Channel 9). It talks more about history, plus business investments and projections for human trials...
The Forgotten Cure - on Sunday Sunrise, Channel 7 - 
plus a short clip on phages from Channel 9
More on this later this week - for now, check out the videos and let me know what you think, including your own questions and concerns about this kind of medical treatment. [CO note: Continue reading part two of this series, "Phage Therapy and Borrelia burgdorferi".]
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Friday, April 15, 2011

0 The Friday Four

In this edition of the Friday Four, we'll look at the impact of antibiotics on bacteria in dogs' intestines, how fire-bellied toads can help us fight germs, antibiotic cocktails in wasp cocoons, and the effect of stress on your gut flora.

1) Impact of antibiotic treatments on bacteria in the intestines of animals

Source Link: http://www.sciencedaily.com/releases/2010/04/100413081238.htm

ScienceDaily (2010-04-13) -- Recent research from Norway has found that resistance to antibiotics is on the increase in intestinal bacteria in animals as a direct result of antibiotic treatments. The antibiotics also alter the composition of bacteria in the intestines. These discoveries provide more knowledge about the undesirable effect of antibiotic treatments and are of comparative interest as regards other animals and humans.

Comments:

This article is about how within a few days of antibiotic treatment, healthy dogs had a lot of antibiotic resistant E. coli bacteria in their intestines. I shudder to think of the state of my own intestines, after many months of antibiotic use.

I don't know if I really have much to say here, other than to say this: The article quoted nearly 50% of all worldwide antibiotic use is veterinary - I wonder what percentage of that 50% is for factory farms and not for people's pets? Antibiotics should be conserved for pets and people on the rare occasion they need them, and this should have been done all along. 

Now we're facing a crisis situation with antibiotic resistance, one which is most readily observed in our hospitals. And not just our hospitals, but our kitchens...

This was the eye-opener today:

Nationwide study finds US meat and poultry is widely contaminated

Multi-drug-resistant Staph found in nearly 1 in 4 samples, review shows


FLAGSTAFF, Ariz. — April 15, 2011 — Drug-resistant strains of Staphylococcus aureus, a bacteria linked to a wide range of human diseases, are present in meat and poultry from U.S. grocery stores at unexpectedly high rates, according to a nationwide study by the Translational Genomics Research Institute (TGen).

Nearly half of the meat and poultry samples — 47 percent — were contaminated with S. aureus, and more than half of those bacteria — 52 percent — were resistant to at least three classes of antibiotics, according to the study published today in the journal Clinical Infectious Diseases.


Please COOK YOUR FOOD THOROUGHLY.

Other methods of fighting bacterial infections which do not promote resistance must be found.

Which leads us to the next two entries of this Friday Four...


2) Giant fire-bellied toad's brain brims with powerful germ-fighters

Source link: http://www.sciencedaily.com/releases/2011/04/110413121010.htm

ScienceDaily (2011-04-13) -- Frog and toad skins already are renowned as cornucopias of hundreds of germ-fighting substances. Now a new report reveals that the toad brains also may contain an abundance of antibacterial and antiviral substances that could inspire a new generation of medicines.

Comments:

So the "germ-fighting substances" they're talking about are peptides. Many of these peptides were shown to be homologous to hormones and neurotransmitters of mammals. And in recent years it has been shown that these secretions also contain a multitude of antimicrobial peptides.

So in the original research report above, 79 antimicrobial peptides were found to be encoded by 158 cDNA clones from B. maxima (the giant fire bellied toad - see photo to left) and B. microdeladigitora brain cDNA libraries, and of those 79, 20 were the same as ones which had been found before - but 59 were previously unknown and new antimicrobial peptides. These peptides worked against Gram-positive and Gram-negative bacteria and fungi.

Earlier research on these other amphibian-derived peptides have shown that some have activity against mycoplasma infections, HIV, and Staphlococcus aureus.

Antibiotics have been derived from peptides for many years now - some synthetically, like polymyxins and bacitracins - and some are natural, nonsynthetic antibiotics, like melittin (which peptides had to be derived from - melittin itself was not used due to its hemolytic properties) and manuka honey itself.

The latter group rely on observing natural host defenses (as nature’s antibiotics) and the clinical potential of peptides derived from these natural sources - amphibians, insects, mammals, and plants - is something that continues to be studied. These natural antibiotics may replace more of our currently existing selection of antibiotics due to increasing resistance.

Source Reference:
Rui Liu, Huan Liu, Yufang Ma, Jing Wu, Hailong Yang, Huahu Ye, Ren Lai. There are Abundant Antimicrobial Peptides in Brains of Two Kinds ofBombinaToads.Journal of Proteome Research, 2011; 10 (4): 1806 DOI:10.1021/pr101285n

3) Bacteria in wasp antennae produce antibiotic cocktails

Source link: http://www.sciencedaily.com/releases/2011/04/110411194823.htm

ScienceDaily (2011-04-12) -- Bacteria that grow in the antennae of wasps help ward off fungal threats by secreting a 'cocktail' of antibiotics, according to researchers.

Comments:

Who knew that a particular wasp - the beewolf wasp (weird name?) - could have something in common with Lyme disease patients?

These crafty little buggers have their own prophylactic antibiotics right on the outside of their cocoons, so that they are protected from disease when they are transforming from larvae into wasps.

Female beewolf digger wasps cultivate symbiotic Streptomyces bacteria in unique antennal glands and secrete them into their larval brood cells. Then the larvae take up the bacteria and weave them into the cocoon while spinning it. The result is a cocoon which produces at least 9 different antibiotic and antifungal substances.

The article makes a statement that reflects the fact that a number of LLMDs have been ahead of the curve when it comes to treating infections. It states:

"A similar combination prophylaxis (also known as combination therapy) approach is increasingly used in human medicine. Such a treatment exploits the complementary action of two or more antibiotics. It results in a higher efficacy against a broader spectrum of pathogens and is known to prevent micro-organisms from developing resistance to the antibiotic substance."

There is a logic behind combination antibiotic treatment - testing and documenting the efficacy of such combinations goes a long way to supporting long-term antibiotic use where it is needed, especially if lack of resistance can be shown.

The beewolf larva hibernates for several months in its cocoon before the 
adult insect hatches. Antibiotics on the surface of the cocoon, produced by symbionts, guarantee protection against microbial pests during such a protracted developmental stage. The amount of antibiotics was visualized by means of imaging techniques based on mass spectrometry 
(LDI imaging) and merged as pseudocolors onto the cocoon.
Credit: Johannes Kroiss and Martin Kaltenpoth, MPI for Chemical Ecology, Jena (Photomontage).

Source reference:
http://www.sgm.ac.uk/default.cfm

4) Don't Stress - It messes with your gut flora

Source Link: http://researchnews.osu.edu/archive/immunegut.htm

Research out of Ohio State University informs us more about the value of the mind-body connection in affecting our health.

Stress not only sends the human immune system into overdrive - it can also wreak havoc on the trillions of bacteria that work and thrive inside our digestive system. New research suggests that this may be important because those bacteria play a significant role in triggering the innate immune system to stay slightly active, and thereby prepared to quickly spring into action in the face of an infection.

So this is what the study was about:
For two hours daily for six days, an aggressive mouse was placed in a cage of a group of more docile, laid-back mice.

At the end of the string of experiments, blood samples were taken from both stressed animals and matched mice from a control group, along with samples of material from inside each animal’s intestine. The blood samples were analyzed to detect the levels of two biomarkers used to gauge stress – a cytokine called interleukin-6 (IL-6) and a protein called MCP-1 that summons macrophages, or scavenger cells, to the site of an infection.

From the intestinal samples, Bailey’s team could determine the relative proportion of at least 30 types of bacteria residing there.

“We know now that if we knock the population of bacteria down with antibiotics, we don’t have the same innate immune response,” Bailey said. “That showed that the bacteria are involved in the ability of stress to prime the innate immune system.”

Compared to the control mice, the stressed animals showed two marked differences: The proportion of one important type of bacteria in the gut – Bacteroidesfell by 20 to 25 percent while another type – Clostridiumincreased a similar amount. Also, levels of the two biomarkers, IL-6 and MCP-1, jumped 10-fold in the stressed mice, compared to controls.

The researchers then treated stressed mice with broad-spectrum antibiotics that could kill as much as 90 percent of the intestinal bacteria for a short period. When they again looked at the two immune biomarkers in the stressed mice, they saw only a doubling of IL-6 and MCP-1 – an increase only one-fifth as much.
Comments:

Stress really affects the immune system - who knew? It's well-known it does, but what isn't known is exactly how it does this - and what can be done other than to get people out of your life who act like aggressive mice.

There is evidence here that stress increases the population of unfriendly and harmful bacteria, and later on, the use of antibiotics knocks down the bacteria needed to prime the immune system.

Healthy stress management and joy are needed in one's life, even while fighting off illness. Especially while fighting off illness.
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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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Saturday, April 9, 2011

4 Artemisinin and cancer

Yeah, I know, I usually don't post on the weekend... well, here I am - but only for a few minutes.

I keep tripping over that Friday Four article I posted on using artemisinin to treat leukemia cells.

I wanted to see more of the research that's out there, and I found this:

Synthesis and anti-cancer activity of covalent conjugates of artemisinin and a transferrin-receptor targeting peptide. Steve Oha, Byung Ju Kim, Narendra P. Singh, Henry Lai, Tomikazu Sasaki. Cancer Letters. Volume 274, Issue 1, Pages 33-39 (8 February 2009)
Source link:http://www.cancerletters.info/article/S0304-3835(08)00668-X/abstract

Effects of artemisinin-tagged holotransferrin on cancer cells
Henry Lai, Tomikazu Sasakib, Narendra P. Singha and Archna Messay
Department of Bioengineering, Box 357962, University of Washington, Seattle, WA 98195-7962, USA Department of Chemistry, University of Washington, Seattle, WA, USA
Received 2 August 2004. Accepted 25 August 2004. Available online 23 November 2004.
Link to above abstract

Apparently Henry Lai did previous research on the use of artemisinin on cancer, in which the earlier abstract states:
"Artemisinin reacts with iron to form free radicals that kill cells. Since cancer cells uptake relatively large amount of iron than normal cells, they are more susceptible to the toxic effect of artemisinin. In previous research, we have shown that artemisinin is more toxic to cancer cells than to normal cells. In the present research, we covalently attached artemisinin to the iron-carrying plasma glycoprotein transferrin. Transferrin is transported into cells via receptor-mediated endocytosis and cancer cells express significantly more transferrin receptors on their cell surface and endocytose more transferrin than normal cells. Thus, we hypothesize that by tagging artemisinin to transferrin, both iron and artemisinin would be transported into cancer cells in one package."
More recent research that was not done by Lai includes this study on using artemisinin to treat prostate cancer:

Effect of artemisinin derivatives on apoptosis and cell cycle in prostate cancer cells.
Morrissey, Colma; Gallis, Byronb; Solazzi, Jeffrey W.a; Kim, Byung Juc; Gulati, Romane; Vakar-Lopez, Fundad; Goodlett, David R.b; Vessella, Robert L.af; Sasaki, Tomikazu. Anti-Cancer Drugs: April 2010 - Volume 21 - Issue 4 - pp 423-432
Source Link: http://journals.lww.com/anti-cancerdrugs/Abstract/2010/04000/Effect_of_artemisinin_derivatives_on_apoptosis_and.9.aspx

An excerpt from the above abstract states:
"Artemisinin is a plant-derived anti-malarial drug that has relatively low toxicity in humans and is activated by heme and/or intracellular iron leading to intracellular free radical formation. Interestingly, artemisinin has displayed anti-cancer activity, with artemisinin dimers being more potent than monomeric artemisinin. Intracellular iron uptake is regulated by the transferrin receptor (TfR), and the activity of artemisinin depends on the availability of iron."

I also found an entire chapter of a book devoted to the study of artemisinin and how it affects pathogens and cancer:

Chapter 18: The Anti-Infective and Anti-Cancer Properties of Artemisinin and its Derivatives. Christopher Paul Hencken, Alvin Solomon Kalinda and John Gaetano D’Angelo. Annual Reports in Medicinal Chemistry. Volume 44, 2009, Pages 359-37
Link (doi): doi:10.1016/S0065-7743(09)04418-2

These are only a few examples of research being done out there on artemisinin for cancer... Seems there is an increasing interest in it. I still want to do a little more digging to see where that claim about artemisinin came from Henry Lai: "It's 100 times more specific than traditional chemotherapy. In breast cancer, it's even better."

Specificity in cancer treatment would improve treatment so much and improve the odds of surviving it with fewer side effects. So I'd really like to know more about this.

Artemisinin. It's not just for Malaria and Babesia any more.
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