COPY NUMBER VARIATIONS

Are there GNOMES in our body ?

We humans are ~99.9% identical, even though each of us is so unique, it's amazing that each of us look and feel so different because of that ~0.1%  variation in our DNA. There are different kind of variations that attribute to this uniqueness, one of them is copy number variations or CNVs in short.

You'd probably know my favorite place to find definitions by now if you were following my blogs.... of course Wikipedia.. which defines CNV's as " alterations of the DNA of a genome that results in the cell having an abnormal number of copies of one or more sections of the DNA." There are part of our DNA which get duplicated and some get broken or deleted.... In my imagination, a picture of this sort comes to my mind... our genome is this large text file and some techno Gnomes are deleting, inserting, inverting or copy pasting some random portion of our DNA at any point in our lives.

We all have CNV in our genome which contributes to our heterogeneity thus decreasing the likihood of us resembling each other like the clones in a star wars series...OK so we are all unique that's nice, but what about the fact that some of these CNV's are associated with diseases. Well that's the downside of the CNV's , which is why scientist are interested in them. These CNVs can either increase susceptibility or resistance to disease depending on who gets the good penny and who gets the bad penny.

There are a great number of diseases caused by these CNVs, Cancer being the most talked about in this context since it's a known fact that cancer is the disease of the genome. There are some interesting facts about CNVs like:

• They can be inherited
• They are different in different ethnic groups
• About 18% gene expression variation are attributed to CNVs ( Based on the last literature I had looked upon)
• DNA segment longer than 1 Kb when compared to reference is considered clinically significant CNV
• Some CNVs play role in Drug metabolizing genes (This is one context where the concept of personalized medicine can be talked about)
• Cancer is associated when there is a really instable gross chromosome.

The important question that would come to one's mind when they are interested about CNVs is how to detect these and find them, well the traditional cytogenetic techniques, CGH ,FISH, BAC arrays and SNP oligo arrays are used. In case you are wondering what are these.. you know where to look (Ans:Wikipedia).
 At present Microarrays are considered the gold standard way for doing any kind of experimentation concerned with CNVs. The analysis and clinical interpretation are done using some current practical threshold values. For example Gain of function ( more than adequate proteins are produced )when  > 500kb of DNA is detected  which has some implications.There are a lot of issues using the current methods, primary statistical issues and other biases. The promise of Next gen sequencing technology bring yet another hope for the CNV studies.

The whole genome sequencing paradigm continues to spark many minds and using this approach will bring in a new dimension of experimental techniques and aid the researcher to take the current knowledge to the next level.So much for the facts (that's all I could remember from the seminar I attended today).. well there is rapid progress in discovering more and more of these CNVs and assess their role so as to help scientist and doctor to come up with better ways to treat cancer patients.

METAGENOMICS!!!

It's funny at times to realise how we tend to behave as if we are a single existing entity in this entire universe, knowing that's not true. To make my point more visible, for example today I threw this used plastic cup in the regular thrash can instead of a recycable one, most of us would think it's no big deal (specially not something to blog about..jeezzz!), well if one thinks about the big picture, it might not be so trivial. That one cup could ending up in some part of the world clogging a plant or an animal. I guess the point that I am trying to bring up is that no one lives in seclusion, we are all interconnected not just with fellow members of a species but with hundreds of species around us and within us. Thus it is important for us to realise our responsibility as a member of this big biosphere where we are as important as are other member who range from less than a micron to may be a godzilla in size. And since we were the lucky ones, out of the millions of species to evolve so rapidly and become the dominating organism, it's our responsiblity to do as much as we can to make sure the world can be a better place to live.

I found Metagenomics interesting more from a philosophical point of view, probably was evident from the first part of my blog but that ends here. But as a person who identifies herself with scientific community, I am more or less going to blog about what I learnt from my course and my personal beliefs and ideas.

Wikipedia defines Metagenomics as study of  "metagenomes, genetic material recovered directly from environmental samples" (as copy and pasted!). I pictured this as a scenario where a traditional microbiologist got us from his laminar airflow hood and pulled up his sleeves and said to himself you know what we have advanced way too much in technology so why not use that to study these little guys in concert with their community, from their natural habitat. In other words there may be lot of potential in them in their natural conditions which could be discovered and applied.

In other words through centuries we have found hundred of new organisms, cultured, studied, characterized, applied and did a whole bunch of stuff with them, now we are in the 21st century, we need to think out of the box. All this time we were studying microbes in conditions created by us, but in reality the environment is no where similar to our traditional laboratory and it would mean that we would totally miss out on all those microbes which we cannot culture.16sRNA was great to classify these guys and derive phylogentic relationships, since we came to know that there are many missing pieces of the puzzle and this was due to the fact we were zooming in on microbes which we could culture.
We use traditional molecular biology, microbiology and bioinformatics knowledge and principles to explore this field. We find all those genes that nature has given these organism to may be adapt to it's environement and use them to improve the world. There is a lot to be explore here and hopefully we will find our answer and once we do that it could translate to clean eneregy in the form of biofuels, cleaning up spills and toxics in environment through bioremediation and helps in many more ways.

Will keep updating more and more as I get time.

A Reflection

The story of evolution is very intriguing, deeply researched and it never fails to disinterest me. It kinda always seem to answer the question of existance (For me atleast!). Even though it is hard for many to believe that we have evolved from a bunch of molecules dancing around each other to this really complex organism, our understanding of science tells us that. And we don't have any other well structured belief system that can be proved to come up with any other story. So coming back to the realization of existance with the context of evolution, I feel that we starting, from an unborn child to a 109 year old person are all here for a purpose. It could be anything that we know or do not know, is good or bad  it does'nt matter.. but once having realised that as members of a civilised social dominating group of this planet our effort should be directed in a constructive manner towards establishing a community where all living orgainsms can find their respective niche and live in harmony.

Ignorance can be a curse!

There are countless examples that can prove the above statement, ignorance of our rights gives goons to control us, ignorance of causation of adverse climatic conditions continue to not stop people from wasting resources, Ignorance of what teacher teaches can get us bad grades...just to cite a few. Expanding our knowledge not only helps us to save the day at times but also makes us broad minded... which is very much what this world needs! Eradicating Ignorance can take us a long way in achiving our common goal of making this world a better place.

Will keep posted.