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.

13 comments:

  1. Thank you, thank you thank you!

    Not just for your wonderfully informative blog, but for taking the time to explain the terminology as well. I, for one, truly appreciate your hard work.

    ReplyDelete
  2. Hi Anonymous,

    You're welcome. Thank you for reading along.

    If there is any portion of this that doesn't make sense, btw, please let me know and I will work on rephrasing it so it is better understood.

    So many of the studies Lyme disease/TBI patients read are full of terminology that may be difficult to wade through, and I decided with this outline of the Borrelia book that I would take the time to explain them - they're only going to come up again and again in the future with studies and articles I post.

    I'm thinking of making a master glossary page for this site at some point - even if it's just linking to all the pages which contain terminology.

    Offhand, how much did you know about what was posted above, in terms of Borrelia burgdorferi not being either Gram-positive or Gram-negative - and the information about viral genes being encoded into Bb's plasmids? It's fascinating stuff... I'm now wondering if there are bacteriophages which are lytic to Bb - and not a temperate prophage. How long has this been going on, too - how long has the prophage been involved in Borrelia DNA?

    ReplyDelete
  3. I just picked this book up through inter-library loan, since I don't have $300+ to drop on a book.

    It is very interesting to say the least...in many ways :)

    I do wish I had my own copy to mark up and highlight. One thing I noticed was that the introduction states the rash occurs in 80% of patients. Then, on page 8, those authors state, regarding the initial cases in Connecticut, that "one-quarter of the patients had developed an erythematous cutaneous lesion..." HUGE difference.

    ReplyDelete
  4. jjbluemountain,

    Welcome to Camp Other.

    I usually don't comment on weekends, but I have some time now.

    Glad to hear you were able to get hold of the book - it is interesting, isn't it? There's so much to read there, too.

    And you're right, there can be some inconsistency in the book. Good job pointing that out.

    Let me know what you think about the rest of it and if you get through the immune response and molecular biology portions of it. I'd be interesting to hear of any insights you have.

    ReplyDelete
  5. CO,

    I made it through chapter 2...I have lots of notes and questions.

    Not much time to type...my major question is: are those prophage particles viable? And, what kind of cells are they capable of infecting?

    Lots to think about, and more researching I will be doing.

    ReplyDelete
  6. jjbluemountain,

    I don't have a lot of time today, either, so I apologize for my short response.

    There are a number of papers out there which discuss the bacteriophage of Bb. Earlier than Eggers et al, Barbour did some research and the phage was found to be a B3-like phage (similar to one that is in other bacteria). Check out the genetics section of this paper: http://mmbr.asm.org/cgi/reprint/50/4/381.pdf

    I would definitely look at Eggers et al paper, and scour Google Scholar for more information.

    I'm not sure what you are implying with your use of the term "viable" above? According to Alan Barbour (see above paper), the phage can go into a lytic stage and kill Bb. I have no evidence so far that it does anything to the bacteria's host. More recent papers state the phage is temperate and makes up Bb's plasmids, and its presence can contribute to Bb's virulence.

    I'm looking for something more recent and specific than papers I read months ago myself.

    ReplyDelete
  7. jjbluemountain,

    Okay, I spoke too soon - just reread the passage above. The implication is that there might be a lytic process going on in Bb. To quote the above paper:

    "A resident virus which under certain conditions enters a
    lytic phase and lyses cultured cells may be the explanation of
    a phenomenon noted by early cultivators of borreliae. These
    investigators found that some cultures had a periodicity to
    them (9, 172, 179, 248). Following logarithmic growth of the
    culture, there was a sudden and steep reduction in the
    number of spirochetes present. This was usually followed by
    an increase in the number of cells in the medium again. The
    "lysis" was probably not, therefore, a direct result of
    nutrient depletion or build-up of toxic substances."

    Look for more recent publications to confirm this. All I've heard of its phage is that it's temperate.

    ReplyDelete
  8. CO,

    Thanks for sharing the link above, I will look closer at it when I get a chance (and also check for more recent publications to see if any have investigated this further). I'll be broadening my scope by requesting a book on bacteriophages, in addition to the one on cell wall deficient bacteria that is on it's way to me (by Lida Mattman).

    It may seem elementary to virologists or others, but, I know who decided that bacteriophages can only infect specific bacteria, and if anyone has verified that is the case.

    I have not made it to the immunology information yet.

    I only found one part of the book that briefly addressed the L-form, or what they call "blebs" on pages 155-156. So, at this moment I wonder, are the L-forms stable or unstable. I wish I had all day to study this, but I don't LOL.

    This book just makes me have more questions.

    ReplyDelete
  9. jjbluemountain,

    No problem. I think one thing to find out that I haven't is how many different phages are involved here - there are different phages for different strains.

    See: http://www.ncbi.nlm.nih.gov/pubmed/8219501 which is from 1993, but indicates that 2 different phages were found for Bb in this experiment, one A-1 and one B-1. Not the B-3 like phage Barbour reported seeing.

    What do you mean by "you know who decided that bacteriophages can only infect specific bacteria"? I'm not sure I'm following you there.

    ReplyDelete
  10. CO,
    Sorry!

    My comment was supposed to say "I would like to know who decided that bacteriophages can only infect specific bacteria, and if anyone has verified that is the case."

    If you look at the diagram on page 33, there are possibly a lot of phages in a single bacterium. On the left of the plasmid drawings it says "phage genes?" And on page 32 lp28-2, lp54, lp56 also say "phage genes?" in their drawings.

    ReplyDelete
  11. jjbluemountain,

    I don't have the book on hand myself right now, so I can't check it out. I had a stack of books here which were on loan from more than one person and I had to return them - I haven't bought the book, either.

    Since you have it on library loan, I suggest finding the most useful-to-you sections and photocopy them before giving the book back, and make notes on sections where photocopying seems less important (like shorter passages). Photocopying citations would be useful, too, as you can seek them out after you have to return the book.

    From what I recall reading from more than one source, the plasmids pretty much are prophages across strains - but I'm not sure which prophages they are. Read the rest of that section... there might be something there on this.

    ReplyDelete
  12. I realize this is a very old post for you, but I'm gonna comment again anyway ;)

    I returned the book, I didn't have near enough time with it, lol.

    I copied a few things I want to study further.

    I have to say, it is certainly full of information.

    What I am left with is...there needs to be more REAL research done on this pathogen.

    more research on how the organism changes its cell wall proteins...

    more research on the function of the prophages...

    more research on the L/cell-wall-deficient forms...

    more research for tests to identify infections...

    Unless someone really important gets involved in this, I don't see any extra money being spent on more research.

    People talk about the controversy being about long-term antibiotics...yes, but what I also think is that IDSA/CDC/regular MDs cannot wrap their mind around the number of people being infected. They don't even acknowledge positive tests, how are they ever going to believe people can have negative tests?

    If a person with a positive test can't even get appropriate treatment, and is told it isn't Lyme, how will we ever get more research done?

    I thought it would help me to know my enemy, instead it made me more depressed.

    ReplyDelete
  13. How can I comment on that much of "stuff" / information in very limited space? I'll try...
    --- "Toxins": I tried to fight this myth / disinformation about a dozen years ago on a German discussion board. As a "camp others" we should not believe everything, even if ?regurgitated a thousand times...

    --- "Herxheimer": that's another myth / disinformation, as far as I can judge. I NEVER experienced anything of that sort. (On a German "Lyme" page someone did a lot of literature research and came up with a psychogenic explanation: I you FEAR such reaction you will (or may) experience them.)
    The top expert Dr. N. Satz from Switzerland with experience with THOUSANDS of "Lyme" patients clearly states that "herxing" is not to be expected...

    --- Of course B.b can survive antibiotic courses, at least in the CNS! Or intracellularly, if an AB is used that is polar and does not reach the intracellular space! (Own experience: With two VERY expensive i.v. courses of Ceftriaxone my cardiac arrythmias persisted. But when I got 50 x 100 mg doxycycline (which is lipophilic, enters cells) and took 300 mg/d the arrythmias disappered - after full 5 years. I suspect that a few B.b within cardiomyocytes can cause arrythmias, in principle only one within one heart muscle cell! No serological reaction = "seronegative" -- but doxy cures this "micro-infection"...)

    --- Understanding your enemy is good, but fighting it down to a level where it no longer causes (major or appreciable) trouble is better, is what is needed.
    I for my part obviously have succeeded with a 2-day "pulse" of doxy every month for more than a dozen years by now - see my comments in your section "Finding the Right Treatment".
    To me it is MUCH MORE IMPORTANT now to concentrate on matters like MS, ALS, Parkinson's and dementias: There is much information that NB (neuroborreliosis) is the root cause: if true all these devastating diseases may be stopped. (Just a few names: MS -- Prof. Gabriel Steiner 1883-1965; ALS: online-book by Sarah Vaughter; Parkinson's -- W.Kohlhepp et al. ca. 1989; Alzheimer's: PD Dr. Dr. Judith Miklossy, whom you are aware of.)
    Doxy is first choice (not for children), including NB (proven time and again in Sweden). I suggest to test my "pulsing" scheme - AND: keep the iron stores in your body as low as in healthy children, because iron is central in neurodegeneration...
    chen-men

    ReplyDelete

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