Dear Friends,

As you can see in our “beautiful creature” on the right, we have a picture perfect example of symbiosis in action. Within our gastrointestinal tract we will see further examples of symbiotic relationships between species; relationships between our human cells and our lumenal microbial population.

As we did last week, we will look a bit more deeply into concepts and terms needed to understand the workings of the human GI tract ecosystem.

The study of life, Biology, is built around the science of taxonomy, the classification and categorization of life forms. Aristotle, the 4th century BC Greek philosopher is considered to be the Father of Biology. He divided organisms into two groups; plants and animals, and divided animals into blood and bloodless. He also divided animals into three groups according to how they moved—walking, flying or swimming. His system was used well into the 16th century. Carolus Linnaeus, an 18th century Swedish scientist classified plants and animals according to similarities in form. He gave us the binomial nomenclature system of genus and species, which is the classification we use today.

Presently, we have advanced into a more accurate way of classifying life forms; the genes of the species through oligo-nucleotide sequencing, by analysing 16S rRNA. In order to understand the 16S rRNA gene we need to review genes in general: What do nucleotides and aminoacids have in common? Why is the ribosomal gene 16S rRNA used for classification?

Nucleotides are the building blocks of DNA (nucleic acids), while amino acids are the building blocks of proteins. The genetic code dictates how a particular nucleotide sequence specifies a particular amino acid sequence. Each human cell is estimated to have approximately 20,000 genes, and each gene is capable of producing three different proteins. Therefore, a human cell can produce 60,000 different proteins. Bacterial cells typically have around 3000 genes, but in bacteria each gene can only produce one unique protein. Thus each bacteria produces 3000 different proteins. Scientists now hypothesize that the 500 different bacterial species in the human GI tract are capable of producing two and half times more distinct proteins than the sum total of the human body cells.

In essence gene expression is to read the information encoded within DNA and us that information to direct the production of the correct protein. In the first stage called transcription, a mRNA molecule is synthesized from a gene within the DNA and is used to copy the nucleotide sequence of a particular gene

After transcription, the messenger RNA (mRNA) travels out of the nucleas of the cell, entering into the cytoplasm, joins to a ribosome where it is then translated into a protein.

(Hang in there; it will make sense when we discuss the Microbiome later)

Scientists are truly at the beginning of this adventure. For every new bacterium sequenced – 10 to 30 percent of the genes aren’t similar to any other species that have even been sequenced before! At this point of our knowledge many of the proteins function is not understood. However, in the newly emerging fields such as Metagenomics, new technology like the 454 Life Science Sequencer, make it possible for the complete characterization of all the species in the human gut. Until recently, the only microbes that were sequneced were organisms that were culturable, and at least 50% of the species in the gut are not culturable. With the new technology the goal of the human microbiome project is to type all the organism in the human GI tract.

16S rRNA is one gene region on the ribosome that has highly conserved regions across all species. For the most part 16S rRNA is uniqually associated with a given species. In summary, each species produces a protein unique to its own species from the 16S rRNA gene, therefore when we analyze the sequence of 16S rRNA we can identify the species.

Next week I will bring the genetics and the microbiome together.

Sincerely yours,

Seann Bardell

BioImmersion.com


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The Last Quiz Answer: This little frog comes from the jungle of Central America. When we talk of de-evolution and the demise of the higher species (amphibians, reptiles and mammals), amphibians are the “canary in the cave”. And, what is the canary telling us?

In a 2003 paper published in Environmental Health Studies two EPA scientists wrote that 60% of the US population is exposed daily to the weed killer Atrazine. Atrazine causes hermaphroditism 100% of the time in lab raised frogs. Similarly, exposed wild male leopard frogs (a common American frog) had reproductive abnormalities comparable to those observed in frogs in the lab. In extremely small amounts Atrazine stimulates an enzyme called aromatase, which converts the male hormone testosterone into the female hormone estrogen. The frogs are chemically castrated because they don’t make testosterone.

Amphibians are in collapse. One-third of the world’s 6,000 species have been put on the endangered list. Ecologists are now telling us that unless we make an “about face” in our use of herbicides such as Atrazine, we will loose as many as one-half of the frog species within the near future. Hormones govern gene expression, and Atrazine is a hormone disruptor. US farmers use 76 million pounds of Atrazine a year.

The possibilities of health benefits that will be achieved by understanding the relationship with our microbiome friends are very exciting. The following article speaks of a new oral vaccine using probiotics: http://www.eurekalert.org/pub_releases/2009-03/nu-gnh031709.php