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

Monday, March 19, 2012

2 Обзор Для русских читателей Лайм боррелиоза

Given what I learned about Russian treatment guidelines for Lyme disease - as well as a particular treatment plan from Serbia - I have decided to offer Russian Lyme disease patients (former and current) a survey.  I plan to give a similar survey to readers from other countries after this one...

Дорогие русские читатели этого блога,Благодарим Вас за посещение и чтение других блогов лагерь.Недавно я узнал от читателя, который лечился боррелиоз Лайма в Сербии, что оба вида антибиотиков выбрали и продолжительность лечения была отличной от той, которую мы обычно получают в Соединенных Штатах.

В результате, мне было интересно, о том, что различные руководящие принципы для лечения боррелиоза Лайма в разных странах. Я посмотрел на принципы Сербии лечения, но не могли найти их в Интернете. Потом я посмотрел на принципы лечения России по боррелиозом Лайма, и я нашел их, и разделяет их.


В поисках русских руководящие принципы для лечения боррелиоза Лайма, я узнал немного о том, как Лайм боррелиоза рассматривается врачей и медицинских вузов России. Я знаю, что мое понимание пациентов ограничен, однако.


Поэтому я хотел бы спросить вас, если вы могли бы пожалуйста, ответьте на несколько вопросов для меня о боррелиозом Лайма. Вы можете ответить с именем пользователя блоггер или быть анонимными - либо все в порядке.


Единственным требованием является то, что вы ни были Лайм боррелиоза в прошлом, или у вас есть боррелиоз Лайма сейчас.


Пожалуйста, ответьте на вопросы ниже, используя следующие инструкции:



1) ответы на русском языке первый, так что поисковые системы будут забрать свой комментарий и больше россиян будут видеть и поощрять участие.


2) Далее ваш ответ России, пожалуйста, напишите английский копию ответа так английских читателей, здесь можно понять ваш ответ.(Используйте translate.google.com или иной русско-английский перевод программы вы считаете хорошим, чтобы перевести ваш ответ.)


3) Имейте в виду, что существует предел в 4000 символов для каждого ответа. Если у вас есть длинный ответ, вы можете сделать комментарий.


Пожалуйста, обратите внимание: Все комментарии модерируются, то есть я рассматриваю их, прежде чем отправлять их в Интернете. Там может бытьзадержка между временем, когда вы входите в комментарий, и он показывает на странице. Я делаю это, чтобы избежать случайного спама и маркетинговыхсообщений.



Ну, вот ваши вопросы:


1) Есть ли у вас Лайм боррелиоза в прошлом?


2) Есть ли у вас боррелиоз Лайма сейчас?


3) Какие этапы или шаги Лайм боррелиоза у вас было в прошлом?Сейчас?


4) Было ли у вас укуса клеща и "быки глаз" сыпь?


5) Как долго времени между укусом клеща и лечение антибиотиками?


6) Какие у вас были симптомы?


7) Как долго вы были или вы больны?


8) Какое лечение вы получили для боррелиоза Лайма?


9) Как долго вы используете антибиотики?


10) Какие еще лекарства и методы лечения вы получите за Лайм боррелиоза (не антибиотики)?


11) После лечения, как здорово ты? Есть ли у вас остальные симптомы?Если да, то каковы ваши оставшиеся симптомы?


12) Как вы думаете, боррелиоз Лайма может быть хронической инфекции - даже после лечения антибиотиками? Считаете ли вы, никаких симптомов после лечения антибиотиками, свидетельствуют о аутоиммунное заболевание?


Спасибо за ваши ответы.Я понимаю, это очень много вопросов, но важно знать, какие проблемы у пациентов с Лайм-боррелиозом лица по всему миру. После Лайм боррелиоза является хроническим, то становится труднее лечить, и зная, как другие люди справляются с этой болезнью может быть полезным.


PS: Если вы знаете другие русские, которые пострадали с боррелиозом Лайма, пожалуйста, присылайте их сюда и попросить их ответить на эти вопросы тоже.


PPS: Я прошу прощения за использование Google Translate - это лучшее, что я мог сделать.

Dear Russian readers of this blog,

Thank you for visiting and reading Camp Other blog.

Recently, I learned from a reader who was treated for Lyme Borreliosis in Serbia that both the kind of antibiotics chosen and length of treatment was different from that which we usually receive in the United States.

As a result, I was curious about what different guidelines are for the treatment of Lyme Borreliosis in different countries. I looked for Serbia's treatment guidelines, but could not find them on the internet. Then I looked for Russia's treatment guidelines for Lyme Borreliosis, and I did find them, and shared them.

While searching for the Russian treatment guidelines for Lyme Borreliosis, I learned a little about how Lyme Borreliosis is viewed by doctors and medical universities in Russia. I know that my understanding about patients is limited, though.

So I would like to ask you if you could please answer a few questions for me about Lyme Borreliosis. You may answer with a blogger user name or be anonymous - either is okay.

The only requirement is that you have either had Lyme Borreliosis in the past or you have Lyme Borreliosis now.

Please answer the questions below using these instructions:

1) Respond in Russian first, so that search engines will pick up your comment and more Russians will see it and be encouraged participate.

2) Below your Russian response, please post an English copy of your response so the English readers here can understand your response. (Use translate.google.com or another Russian-English translation program you think is a good one to translate your response.)

3)  Be aware that there is a 4,000 character limit for each response. If you have a long response, you may want to make a new comment.

Okay, here are your questions:

1) Have you had Lyme Borreliosis in the past?

2) Do you have Lyme Borreliosis now?

3) What stages or steps of Lyme Borreliosis did you have in the past? Now?

4) Did you have a tick bite and a "bulls eye" rash?

5) How long was the time between the tick bite and antibiotic treatment?

6) What were your symptoms?

7) How long were you or are you sick?

8) What treatment did you receive for Lyme Borreliosis?

9) How long did you use antibiotics?

10) What other medicines and treatments did you receive for Lyme Borreliosis (not antibiotics)?

11) After treatment, how healthy are you? Do you have any remaining symptoms? If so, what are your remaining symptoms?

12) Do you think Lyme Borreliosis can be a persistent infection - even after antibiotic treatment?  Do you think any symptoms after antibiotic treatment are evidence of an autoimmune disorder?

Thank you for your answers.

I realize these are a lot of questions, but it's important to know what problems patients with Lyme Borreliosis face around the world. Once Lyme Borreliosis is chronic, it becomes harder to treat and knowing how other people are managing this disease could be helpful.

PS: If you know of any other Russians who have suffered with Lyme Borreliosis, please send them here and ask them to respond to these questions, too.

PPS: I apologize for using google translate - it's the best I could do.


Image credit:
English: Tomsk I railway station, Russia
Русский: Вокзал станции Томск I, Россия
by Alexander V. Solomin from Wikimedia Commons
This file is licensed under the Creative Commons Attribution 3.0 Unported license.



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Friday, April 29, 2011

4 Top 10 Tips For Doing Your Own Lyme Disease Research

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

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

Examples:

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

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

Examples:

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

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

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


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

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

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

5)  Read educational institution web sites in general.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

And a bonus, Number 11:

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

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

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

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

Happy researching!

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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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Monday, February 21, 2011

7 Patent Watch: VMP-Like Sequences of Pathogenic Borrelia

To the dude that keeps writing in his blog that chronic Lyme patients are hypochondriacs, and to A.C. Steere, who in his March 2010 Powerpoint presentation insisted that there is no such thing as Chronic Lyme Disease and it is a misnomer, I have one question to ask:

If Lyme disease is easy to diagnose and treat and not chronic - as you and the IDSA have stated - why do people in the field put this stuff in a patent application posted December 2010?

Application number: 12/853,019
Publication number: US 2010/0317026 A1
Filing date: Aug 9, 2010

Check it out on Google Patents. You can download it as a PDF file on the upper right corner of your window.

Select snippets for your viewing enjoyment:

First, we'll start with the abstract so you know what they plan to do with these VMP-Like Sequences of DNA, anyway. Oh, vaccines? Why yes. But also possibility of therapeutic applications and in immunoblots as reagents.


If you download and read the entire thing, though, you either need to a) have some focus or b) a little of insanity or c) possibly both to get through it. If you do bother to download the PDF in its entirety, I recommend that you start looking at the early pages and skip over a few pages about a third through, then read again, then skip the DNA sequencing pages at the end - unless you are a molecular biologist or geneticist... then it will be more fun for you to read all of it.



[0006] These organisms are closely related and cause similar manifestations with multiple stages: an expanding rash at the site of the tick bite (erythema migrans), fever, lymphadenopathy, fatigue, and malaise; effects of disseminated infection, including carditis, meningoradiculitis, and polyarthritis; and chronic manifestations including arthritis and neurologic disorders. Lyme disease is often difficult to diagnose because of shared manifestations with other disorders, and it can also be refractory to treatment during late stages of the disease.

re·frac·to·ry
 (r-frkt-r)

adj.
1. Resistant to treatment, as a disease.
2. Unresponsive to stimuli, as a muscle or nerve fiber.

(Did anyone make a checklist out of reading the above symptoms and nod "yes" to them? I did...)

[0007] B. burgdorferi, the etiologic agent of Lyme disease, is able to persist for years in patients or animals despite the presence of an active immune response (Steere, 1989; Schutzer, 1992).


[0009] Lyme disease may be disabling (particularly in its chronic form), and thus there is a need for effective therapeutic and prophylactic treatment. (Noooo...  You think?)

[0010] However, animal studies indicate that OspA vaccination may not be effective against all strains of Lyme disease Borreliae. OspA is also not useful for immunodiagnosis, due to weak antibody responses to OspA in Lyme disease patients. (Wait... but... Lymerix... I thought you guys said you pulled it due to lack of sales? Oh shhhh... that's not what I heard...)

[0020] An important aspect of the invention is the recognition that Borrelia VMP-like sequences recombine at the vls site, with the result that antigenic variation is virtually limitless. Multiclonal populations therefore can exist in an infected patient so that immunological defenses are severely tested if not totally overwhelmed. Thus there is now the opportunity to develop more effective combinations of immunogens for protection against Borrelia infections or as preventative inoculations such as in the form of cocktails of multiple antigenic variants based on a base series of combinatorial VMP-like antigens.


[0127] The present work discloses the identification and characterization of an elaborate genetic system in the Lyme disease spirochete Borrelia burgdorferi that promotes extensive antigenic variation of a surface-exposed lipoprotein, vlsE. A 28-kilobase plasmid of B. burgdorferi B31 (pBB28La) was found to contain a vmp-like sequence (vls) locus that closely resembles the variable major protein (vmp) system for antigenic variation of relapsing fever organisms. Portions of several of the 15 non-expressed (silent) vls cassette sequences located upstream of vlsE recombined into the central vlsE cassette region during infection of C3H/HeN mice, resulting in antigenic variation of the expressed lipoprotein. The resulting combinatorial variation will potentially produce millions of unique antigenic variants and thereby contribute to immune system evasion, long-term survival, and pathogensis in the mammalian host.

(Note: C3H/HeN mice are reported to develop severe arthritis when infected with B. burgdorferi.)




These observations suggest that the vls locus may provide the Lyme disease Borreliae with the capability of antigenic variation analogous to the vmp system of B. hermsii (Barbour, 1993). The above similarities also indicate that the vlsE gene, silent vls cassettes, and large vmp genes of relapsing fever organisms, all evolved from a common ancestral gene. Their relatively high G+C compositions (e.g. 45% for vlsE and 37% for vmp17) when compared with Borrelia G+C content (~28%) are also consistent with this evolutionary relationship, and further suggest the possibility of lateral transfer from other organisms(Okay, these are more "may" and "indicate" and "suggest" statements, but given the weight of the evidence so far... something to consider.)

[0130] Lastly, each phase of B. hermsii infection is caused predominantly by organisms expressing a single vmp allele (Meier et al. 1985; Plasterk et al. 1985), whereas a high degree of vlsE allele variation occurs among organisms isolated even from a small ear biopsy specimen during B. burgdorferi infection.
[0137] Variation of B. burgdorferi surface proteins such as VlsE may also effect the organism's virulence and its ability to adapt to different micro-environments during infection of the mammalian host. Recent studies of a Borrelia turicatae mouse infection model that resembles Lyme disease showed that one serotype expressing VmpB exhibited more severe arthritic manifestations, whereas another expressing VmpA had more severe central nervous system involvement (Cadavid et al, 1994). The numbers of Borreliae present in the joints and blood of serotype B-infected mice were much higher than those of mice infected with serotype A, consistent with a relationship between Vmp serotype and disease severity (Pennington et al, 1997). (And? Where was the Borreliae present in mice in serotype A? Hm?)
[0138] The importance of the vls-containing plasmid, pBB28La, during infection is supported by the following evidence: (i) all high-infectivity clones and strains tested thus far contain the vls-containing plasmid pBB28LA and loss of this plasmid correlates with a decrease in infectivity; (ii) pBB28La was maintained in all animal isolates tested thus far, and (iii) the vls sequences are preserved among three Lyme genospecies despite their genetic heterogeneity (Casjens et al, 1995).

[0139] VlsE (or, potentially, other genes encoded by pBB28La) appears to have another important but undefined function which is unrelated to antigenic variation. Low-infectivity clones lacking the vls-encoding plasmid pBB28La do not propagate in severe combined immunodeficiency (SCID) mice, indicating that the required factor(s) provides an important function unrelated to evasion of the adaptive immune system.

Also, in vivo selection against Bb clones lacking pBB28La appears to occur early in infection (within the first week), before the adaptive immune response would be expected to exert significant selection pressure. Therefore, it is likely that vlsE plays an important role in some aspect of infection (e.g. colonization, dissemination, adherence, extravasation, evasion of innate immune mechanisms, or nutrient acquisition), and that antigenic variation merely permits surface expression of this protein without leading to elimination of bacteria by the host's immune response.

[1041]  A genetic locus (called vmp-like sequence or vls) has been identified and characterized in B. burgdorferi that surprisingly resembles the vmp system of B. hermsii. [...] Examination of ear and blood isolates from C3H/HeN mice infected 4 weeks previously with B31 clone 5A3 demonstrated the occurrence of promiscuous recombination at the vlsE site, such that each of B. burgdorferi clones examined was unique and appeared to have undergone multiple recombination events with portions of the silent vls cassettes. The resultant vlsE variants exhibited a decreased reactivity to antiserum directed against the parental Vls1 cassette region. This elaborate genetic system permits combinatorial antigenic variation of vlsE in the mammalian host, thereby contributing to evasion of the immune response and long-term survival in the mammalian host.
Etc...
[0145] This mechanism of genetic switching appears to be different from any other antigenic variation mechanism described in bacteria or protozoa and has important implications in Lyme disease. By combining different regions of the silent vls cassettes, it is possible for many different vlsE serotypes to coexist the same patient. It may be impossible for the host to mount a protective response against any one of these clonal populations, because of the small number of each type. Even mounting a response against one serotype would not protect against rapidly evolving, new serotypes. The fact that B. burgdorferi has evolved such an elaborate mechanism for varying the sequence of VlsE indicates the importance of the protein in pathogenesis and/or immune evasion.
[0294] Since the C3H/HeN mice were infected with a large number (105)  of the organisms, it was possible that the antibody response against vlsE had resulted from the intial inocolum. To test this possibility, sera from the white-footed mice (Peromyscus leucopus) infected with B. burgdorferi B31 via tick bite and from human Lyme disease patients were used to react with the similar immunoblots. The representative results depicted showed that tick-infested Peromyscus leucopus mice also had strong reactivity to the VlsE protein of B. burgdorferi B31-5A3 and GST-Vsl fusion protein but not with GST alone. These results were further confirmed with sera from Lyme disease patients. [...] These results indicate that VlsE is expressed and is highly immunogenic in the mammalian host, but that genetic variation may generate unique VlsE variants which are no longer fully recognized by the immune response against the parental vlsE. They also indicate that antibodies generated against VlsE may be useful in immunodiagnosis of Lyme disease. (Got new tests, anybody? I hope this is a good thing!)
[0295] (Contains test data that just confirms more of what was said further upstream, but thought I'd add it here...)

Seriously, this is fascinating stuff, and I really hope that the knowledge about vlsE can be put to good use. My immediate thoughts, of course, are to ask how this can be used to create new treatments for Lyme disease and improve testing - as well as if a safe and effective vaccine can be developed. The vaccine issue - as always - is touchy, and is no different in this case... especially when they are proposing multiple shots will be needed over time. Also, there is more detailed information in the remainder of the patent describing ways of using bacteriophage therapy or attaching DNA to recombinant adenoviruses for  gene therapy treatment.

But the take home point I'm making here by sharing portions of this patent (and it is a multipage document, with lots of pages of data and genetic sequencing that most people will not want to plow through) is that Lyme diseases's Borrelia burgdorferi is unique, and closely related to relapsing fever, and has genetic behavior which is similar to - yet different from - relapsing fever.

Borrelia burgdorferi is highly complex in its presentation, multiple sources have stated that it can be refractory to treatment, and it has a chronic manifestation. It's all right here.
"This mechanism of genetic switching appears to be different from any other antigenic variation mechanism described in bacteria or protozoa and has important implications in Lyme disease. By combining different regions of the silent vls cassettes, it is possible for many different vlsE serotypes to coexist the same patient. It may be impossible for the host to mount a protective response against any one of these clonal populations, because of the small number of each typeEven mounting a response against one serotype would not protect against rapidly evolving, new serotypes."
We can't ignore this. The scientific truth isn't going to go away, whether it is posted in this patent or in the papers to which it refers.

ADDENDUM

There are more entries posted here related to this one. If you were interested in this post, check out these  - especially the one on the vlsE test kit package insert:
http://campother.blogspot.com/2011/02/more-on-that-vmp-like-sequence-aka-vlse.html
http://campother.blogspot.com/2011/02/package-insert-excerpt-athena-multi.html
http://campother.blogspot.com/2011/02/history-of-antigenic-variation-in.html
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