Genome and Genome complexity

GENOME
During early 90's, scientists used to define the 'genome'as complete set of genes of an organism. Later with the discovery of non-coding, repetitive and transposable elements, the word start to loose its original description. Now the content of the genome in eukaryotic cell system can be described under three terms viz. 'genome', 'transcriptome' and 'proteome'. Though the original definition for 'genome' still holds good for prokaryotic cell systems, while applying the same term for eukarotic cell system, we use in a more general sense as 'the complete sequence of DNA of an organism'. One can not determine the full content of the genome by considering either total mRNA content of the cell or by considering the polypeptide chain of the protein. The reason is, all the genes may not be expressed in all the times uniformly in all the cell types within the body; all the RN A's may not be used for protein synthesis, for example in Mouse having the genome size 2.5 billion base pairs, about 60% is used for RNA synthesis and out of it less than 5% is used in protein synthesis; and another important reason is that during co and post translational process, intact protein is trimmed or spliced into smaller fragments. By realising these facts, the term 'genome' is used in a more general sense as 'complete sequence of DNA of an individual'. The term 'TRANSCRIPTOME' is used to describe 'the complete set of gene/RNA expressed in one particular time and cell system'. It includes the sum of all types of RNA's like mRNA, tRNA, rRNA, snurp's(small nuclear ribonucleo protein particles) and scyrp's(small cytoplasmic ribonucleo protein particles) found in one particular time and cell system, and even it can also extend to the level of organism. On the other hand 'proteome' describe the complete set of polypeptides found in a cell. Though, the proteome value is alwaysless than the transcriptome, there should be a close correlation between the two values in any particular conditions.

The study of DNA reassociation kinetics reveals that, the eukaryotic cell system is made up of three types of sequences, they are

1. Highly repetitive
2. Moderately repetitive and
3. Non-repetitive

Non of the sequences of category 1 and 2 codes for protein and completely absent in prokaryotic cell system. Hence, prokarotic genomes are said to be as more complex than eukaryotic cell system.

DNA reassociation kinetics: When denatured DNA allowed to renature, it proceeds with three different pace i.e. highly repetive sequences rewind very fast(fast component), followed by moderately repetitive sequences(intermediate component) and finaly the unique sequences (Slow component) as mentioned in the figure. It can be determined by using the formula

C/C0 = 1/(1+kC0t)........................................................................................equation 1

for half completion, equ. 1 becomes

C/C0 = 1/2 = 1/(1+kC0t1/2)

so that

C0t1/2 = 1/k

Since, C0t1/2 is the product of concentration and time required to proceed hlaf way, a greater C0t implies a slower reaction expressed in nucleotide-moles x seconds/litre.

If the number of sequence present in fewer copies, then the reaction becomes too slow, C0t value becomes very high and genome can be said to be as more complex and vice versa.

Genome complexity can be easily calculated by using the formula:

Cot 1/2(DNA of any genome)/Cot1/2(E.coli genome) = (complexity of any genome)/4200000bp

Where, genome size of E. coli is 4200000bp and its Cot1/2 value is '9' is used as a standard as it contains 100% unique sequences.

therefore,

Complexity of the genome (x) = (C0t1/2 of 'x' X 4200000 )/9

One can also calculate the complexity of other genomes by using the C0t1/2 values from the table above.

References:

1. Benjamin Lewin, GENE V and X

2. http://mol-biol4masters.org/DNA_C_Value_Paradox2-Hybridization_Kinetics_files/image007.jpg

3. http://www.ucl.ac.uk/~ucbhjow/b241/images/cot_curves.jpg

Around the man who uproot the divine pole of human civilization

As we know, we all the descendent residues of our ancestors since the beginning of human evolution. During the course of evolution, our attitudes, thinking, mode of life and tastes were all refined to set maximum fitness in this competitive ecosystem. Beliefs on god and their worship specific to different parts of the world and in different religions were all remarkable contributions of our ancestors and still followed by majority of people in spite of the vast achievements made in different fields of science and technology. The logic behind it was quite interesting that one cannot be easily removed or neglected in the name of scientific proof. Our ancestors by realizing the human’s possible tendencies and future probabilities of our own existence, they succeed to build highly constructive and logic framework and also carefully carried forward to maintain their continuity of generation. As a consequence, during the course of time these logic and beliefs acquire new dimensions and ultimately leads to different religions, cultures and communities. Out come of all these revolutions occurred during the evolution of human civilization are the present day generation and also the associated developments, knowledge and achievements. In any system, one can realize both positive as well as negative aspects that prevailed as a part of the system itself. The effect of this difference is maximized when the population is highly heterogeneous like India and it acquire medium pace in the countries having almost nearly homogenous population. Of course there are so many factors associated with it but it is not suitable to discuss here. In our purana’s and veda’s also, there are so many quotes were recorded especially in BHAGAWATHGEETHA, during those days itself our ancestors knew the fact about the universe as ‘whole and soul’. But the way they expressed in front of the common people was sensibly remarkable, they maintained it to close the eyes of common people partially so that they didn't loose the interest about their tradition, culture and moral responsibility to continue their generation!!!

Now recently the ultimate theoretician Stephen Hawking, the mathematics professor from Cambridge University disclosed the fact as "This Universe is not created by the god or in other words, God is not required for this universe". His argument is 'universe has the capacity to create anything from the vaccum/space'. Yes, as per the present day developments and information obtained from big-bang experiment (?), what professor said was right. I would like to quote the statement made by the great evolutionist by name Theodosius Dobzhansky. He says that ‘the theory of evolution was handicapped due to discontinuity of information’. Discontinuity refers to our life span, at the most we can live on an average for about 70years, whatever the observations made by us is restricted only to small fraction of our own life span. As far as the universe is considered, its quite likely seems to be as, each and every species has their own universe, like that we the humans see the universe according to our own way and ability. The unit of each and every activity in the universe demand millions and billions of years and probably this much duration is sufficient for our surrounding environment to create and to extinct 100’s of species like us. Of course extinction can take millions of years or even a fraction of minute is sufficient.

Now, the question still remained as miracle, whether science or social belief?

by

A RAMESH