Oh snap, what’s a SNP?

A Single Nucleotide Polymorphism is a change o...

A Single Nucleotide Polymorphism is a change of a nucleotide at a single base-pair location on DNA. Created using Inkscape v0.45.1. (Photo credit: Wikipedia)

OK, I don’t like it either, but scientist use so many big words and then they use so many acronyms and often think that the rest of the world uses them also.  Not only does the rest of the world have little clue about what most of them talk about, they certainly don’t know/understand/recognize the acronyms and terms.  There is said it.  Let angry scientist yell at me…won’t stop it from being true.

So, today I thought I might demystify (if possible) a term we use all the time and in this case, an acronym also.  SNP.  SNPs stand for Single Nucleotide Polymorphisms.  What?  Yes, they are a single change at the nucleotide level (one of the four letter codes that represent the entirety of our DNA, an A,C, T or G) of the DNA.  You might have heard about a mutation, which can also be a result of a change at the single nucleotide at the DNA level also.  Let me explain.

We have over 3 billion nucleotides that in essence make up the entirety of our DNA makeup.  You and I are different, so we express that DNA differently, but essentially we all have quite a similar 3 billion sequence code.  The DNA is where our functional proteins come from, although the steps to get from a piece of DNA to a protein is quite complex.  You get your DNA from your mom and dad (a combination of them) as your parents did from their parents.  So, you see, the DNA is going to be different in all of us as the mix we get from our parents is unique.  But, in general all of us who get blue eyes (let’s keep blue simple..but we know there might be many shades of blue) essentially have the same blue pigment at the DNA level and thus code for a blue protein (pigment).  Now, let’s say there is a random mutation that changes one nucleotide (again the building blocks of the DNA itself) in the blue gene.  That mutation might result in no color being made, or a different color, or even the same color if the mutation is in an unimportant part of the gene.   The point is that this mutation is random.  And it might not even occur in the cells of the eye or not even in the cells that will be given to your offspring.  It means that that mutation would only be passed down to future generations if it was in the sex cells (sperm or eggs).  If not, than it is random and a single incident mutation.

A SNP on the other hand is handed down.  It is a single nucleotide change that sticks in the chromosome (the way the DNA is bundled together….the structural unit of DNA) that is passed down through subsequent generations.  So, a SNP is a change that is maintained at the genomic level.  Have you ever heard that you can not simply give your organ to someone else, as their body may very well reject it.  Well, that is due to the presence of SNPs in the genes of the body that are known as transplant antigens.  So, your mom and dad gave you a mix of their own SNPs in their transplant antigens and you will give your future offspring a unique mix as well.  However, overall in a population, a certain number of SNPs will be present.  In other population, let’s say Asia, another set of SNPS are more frequent.  A SNPs is not a random mutation.  It is a difference in the nucleotide level (a single one) in the population due to mixing of that population over time.

So for transplants (giving someone your liver for example) you can only give the organ to a person who has the exact same set of polymorphisms in your transplant antigens.  If you have different ones that the recipient, then they will likely reject your liver (or rather their own immune system will try to remove it).

SPS are found all over the genome.  The one’s I was referring to above are functional, they actually have a known consequence.  There are many other SNPS that lie in regions where there is no known function (for example that do not code for protein).  However, if you read my post last week, you will note that those regions may not be junk at all and may be functional…in ways we don’t fully understand yet.

In summary, SNPs are single nucleotide changes that are in the DNA that are acquired by hereditary properties and exist in groups of people in a population.  Some may be functional and some non functional.  They are not mutations in that they are not random and must be inherited.  Over millions of years, some SNPS can be lost, but usually the whole set of SNPs in the genome are thought to be kept in the population (as long as the population does not die-off of course)!

I hope that was helpful and the next time you see SNP will you feel a tad bit more enlightened.

Dr. C

 

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The new human genome!

A slight mutation in the matched nucleotides c...

A slight mutation in the matched nucleotides can lead to chromosomal aberrations and unintentional genetic rearrangement. (Photo credit: Wikipedia)

So this week, in over 30 different journals, a detailed study was reported on the nature of the over 3 billion nucleotides (the fundamental building blocks of genes and thus of DNA) that make up the human genome.  In the turn of this century, the human genome was completely sequenced (identified at the nucleotide level).  At that time it was thought that only 1.5% of those 3 billion plus nucleotides were functional and directly coded for proteins.  Much of the remaining 98.5% of the human DNA material in all of our chromosomes where thought to be junk DNA, thus serving little to no function.

However, this has been challenged greatly by new studies published this week suggested that as much as 80% of all the DNA in our cells are functional.  They define functional as the following: nucleotides that do not code for proteins but that does for RNA that is not translated in proteins (but can be regulatory in nature), nucleotides that themselves bind proteins, or nucleotides that affect the shape of the DNA in one way or another.  Thus is a far cry from the thought that most of the genome in our bodies is junk.

What does this mean in the real world and will it revolutionize medicine and science. It certainly means that labs all around the world working on their favorite gene or gene location will pay a lot more attention to sequences outside of the traditional gene unit (usually includes, enhancer, promoters and the introns and exons of the genes themselves).  More and more data will probably come out from labs on novel regulatory mechanisms from far away gene sequences and so on.  However, clinically t is doubtful that this new finding will bear any direct relevance to treatment and disease.  Just as the impact of the human genome was rather weak after the initial wave of euphoria, this too will pass.

Human genome

Human genome (Photo credit: Wikipedia)

Why medical community still doubts herbal remedies

English: Herbal remedies for sale in San Juan ...

English: Herbal remedies for sale in San Juan de los Lagos, Mexico (Photo credit: Wikipedia)

We have all heard it:  herbal remedies can’t be wrong, they have been used for thousands of years.  In fact, it’s true…many cultures, tribes, medicine men, etc. have been using and in essence prescribing natural plant based herbal remedies for many many years….in fact, much longer than that of modern medicine/pharmaceuticals.
So why then is the medical community reluctant to embrace herbal medicines and remedies.  Although it’s fun to poke fun of doctors, medical administrators, insurance companies, and pharmaceutical executives, the universal distrust in these types of remedies is not unfounded.  Here is a small list of reasons: 1) Many herbal remedies were found to have good affects on one particular ailment (such as stomach discomfort) and then prescribed and suggested to work in other organ system (the liver, lungs, etc.) with little or no evidence.  2) Many herbal remedies have been linked to visual cues in how they were assigned to work.  For example, it is common to find that red fruits or seed products are often given to women for bleeding conditions as blood is red and so is the remedy.  3) Many herbal remedies over the years are assigned to work on various parts of the bodies as they were harvested in certain ways- functional links.  For example, the Cantonese believe that eating pig brain will make you smart, or if you have impotency- eating of dried and ground up ox testicles will help.  Although these are not plant remedies, these types of functional or anatomical links have dominated traditional remedies.  4) The vast majority of remedies, even though many have commonalities from independent groups around the world and have been used by millions, have no properly controlled studies to show that they actually work. 5) They are prescribed and administered in widely varying fashion. The list goes on and on and these objections are fair.  That does not mean that herbal remedies don’t work, it just means we have a long way to go before modern practitioners will embrace them.

The last time that a medical compound was successfully derived from a plant and used in clinical medicine was in 1967.  That agent/drug was Taxol.  That was a long time ago?  For a while people just stopped looking for them.  However, many are now pursuing this newly popular science; namely plant medicinal chemistry with newer techniques.  Who knows, maybe one of our next blockbusters will come from a herb, plant or natural product.   It might not only save lives but also teach us identify the chemical component that works in the plant itself.