Sorcerer II Global Ocean Sampling Expedition

According to the original article, 7.7 million sequenced snippets of sea-born genomic DNA has been collected by the Sorcerer II Global Ocean Sampling Expedition. But, owing to the huge amount of microbial samples, they have a hard time predicting the knowledge and significant purpose the data may bring to the field of science and biology.

This scenario is similar to the experience of Charles Darwin aboard the HMS Beagle on his scientific journey to the Galapagos Islands. Darwin had no idea that his collections will play a vital role on his theory of evolution through natural selection. The Sorcerer II sampling expedition has brought huge amounts of sequences but Gerard Manning, Ph.D. says that this was just the beginning. In the article, he was quoted “We’re starting to explore this trove of sequences now, but it may be decades before we fully understand it all.” He had to filter millions of selected samples for the classification of the identified proteins. Similar to what the famous ornithologist John Gould did in classifying the Galapagos finches that led Darwin on the right track.

The article also mentioned the bright prospect in the use of metagenomics (also called environmental genomics) that allow the researchers to examine genomic snap shots taken directly from the environment. As many as 99% of all bacteria were examined which under the present circumstances can not be grown in a laboratory and then examined using compound binocular microscopes.

Compound binocular microscopes are commonly used in viewing, studying, and identifying bacteria and other microscopic microorganisms. Compound binocular microscopes are light microscopes having two eyepieces.

Expanding the universe of protein families
A group of scientists, as mentioned in the original text, headed by Shibu Yooseph, Ph.D. collected a whole grab bag of bits and pieces of genomic which required the use of new methods to extract meaning. The DNA fragment were examined with another and produced clusters of related sequences. The Global Ocean Sampling Expedition (GOS) made an exhaustive analysis and predicted more than 6 million proteins in their data which served as the basis for future studies. They made almost 350 million comparisons surpassing any others done before by two or more in magnitude.

The article also mentioned a hardware called the Time Logic that was used by the research team. The hardware accelerates the genomic searches. Time Logic is a bio informatics program developed by Gerard Manning and Yufing Zhai of the Razavi Newman Center which accelerated their work in two weeks, a task that takes a conventional computer to do in over a century. They also discovered, with the use of compound binocular microscopes, that the hardy spores found in gram-positive bacteria no longer exist in the marine-borne bacteria. The flagella, a whip-like extension used for genetic exchange between them is also rarely frequent. The article mentioned that this comparison of data with the Yooseph clusters had led to a discovery of hundreds of new genes not previously known before.

Diversity of Microbial Kinases
Manning, Yuyeng Zhai, the bioinformatics programmer, Natarajan Kannan, postdoctoral researcher and Susan S. Taylor, Ph.D., zoomed in on Kinase, an enzyme that control every aspect of eucaryotic cell biology. The eucaryotic cell can be seen using a compound binocular microscope. The study group attached phosphate group to them to control the activity of proteins.

With the GOS data for bacterial Kineases, under their disposal, they dug up 45,000 protein Kinase sequences that fell into 20 distinct families. Out of which the eucaryotic protein Kinases are just but one and the others make up a wide range that included several others not yet described before.

Previously, prokaryotic protein-like Kinase was considered to be not very close to the limelight in the group but according to Manning they are even more prevalent than histidine kinase. It is thought that bacteria rely mostly on histidine kinases for their signaling needs but structurally, they are different from protein kinese.

Although kinase family varies in their sequence, 10 key residues are contained in the core of all the kinase families, seven of which has been previously known, the others were a surprising find. They were innovative families that even with the core residues they manage to eliminate all but one of the 10 key residue. According to Natarajan Kannan the loss of one key residue can be compensated for the changes around conserved regions of the protein. Most importantly these changes are also observed in human Kinases.

The article has also mentioned that these researches were funded by the Razari-Newman Foundation. Foundations such as this has helped many researchers in their pursuit of knowledge.