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I can recognize when I am over my head! Please help me understand this:

Antibodies against OspA epitopes of Borrelia burgdorferi cross-react with neural tissue

http://www.sciencedirect.com/science?_o ... 9ebac2011e

Neurological sequela of chronic Lyme disease include
encephalopathy, myelopathy and peripheral neuropathy.
These have generally been attributed to either persistent infection
or pathogen-induced autoimmunity. In this study, we investigated
the presence of cross-reactive human neural epitopes that share
amino acid sequences with Borrelia burgdorferi OspA protein.
Sequence similarity analysis was carried out by searching known
cDNA sequences from brain tissue. The cDNA database search
yielded three sequences that were identical to sequences in OspA.
Corresponding peptides were synthesized and antibodies were
generated against them in rabbits. Antibodies against two of the
homologous OspA peptides were found to react with neurons in
human brain, spinal cord and dorsal root ganglia by
immunohistochemistry.

The cDNA library from brain tissue is complementary DNA, i.e. corresponds to the RNA sequences that can be generated from the genes in a brain cell. So when a gene is expressed, enzymes copy the gene's DNA into an RNA copy called an RNA transcript. This then gets spliced down to a messenger RNA, removing unneeded sequences in the gene called introns (intervening sequence) and splicing together the remainder portions which are called exons (expressed sequence).

The messenger RNA (mRNA) is translated into a polypeptide (a chain of amino acids) by the ribosomes. The polypeptide folds into the protein which then is functional or perhaps gets a few post-translation modifications to make it functional.

The RNA code for each amino acid is in groups of three bases, those bases being symbolized as A, U, G, or C. Each combination of three bases equals one of the 20 amino acids. There is some redundancy in the third base so that AGU = the amino acid serine, and AGC = serine also. AUG = the amino acid methionine.

So what the authors did was determine what RNA sequences would generate the protein and then they searched the cDNA library to find if there were any sequences that corresponded. They found some sequences but didn't know immediately what they were.

They use DNA rather than RNA because RNA degrades very easily. And they used cDNA corresponding to the gene messages because they didn't want to search all the human genome DNA sequences, a lot of which does not code for proteins.

They then used the matched sequences to generate proteins or portions of protein and raised antibodies against this in rabbits by injecting the proteins into rabbits along with some adjunct compound that irritates the rabbit's immune system into a reaction. They then collected antibodies from the rabbits and used those to stain cells to see what type cells and where the antibodies bound. They can also run immunoprecipitation assays to pull down the specific proteins and try to characterize them. They can eventually gather enough information to figure out what protein it is in humans.

So what they might be suggesting is that an earlier infection with the bug exposed the person to a lot of the bug's protein, which happened to be similar to the human. This provoked an ongoing reaction to the human protein. I could only read the abstract so I don't know if they concluded that there is an ongoing infection with the bug. I guess they were suggesting both might be possible, ongoing reaction to human protein or ongoing infection with the bug.