Bangalore scientists help breakthrough in human genome studies

Two independent research bodies have almost simultaneously announced that they have created drafts of the human proteome, which is the protein equivalent of the human genome. One of the drafts was created by researchers in Bangalore; the other originated in Germany.

The research team from Bangalore mapped proteins coded by 17,924 genes, which is about 84 per cent of all genes that are known to code for proteins.

"India is at the forefront of proteome research," scientists from the Institute of Bioinformatics (IOB), Bangalore, said at a press conference. "We weren't involved in the human genome project, but we are leading the world in creating a complete database for proteins."

"It is a surprising co-incidence that both of our groups have simultaneously worked on this (proteome draft) without knowing each other's work," said Dr Harsha Gowda. He led the team from Bangalore along with Dr Keshava Prasad, also from IOB.

Proteins are complex molecules that are made by the cells in the body using instructions from genes. The Human Genome Project had created ripples in the scientific community back in 2003 by allowing researchers to look for specific genes that were involved in development or disease. The new directory will help scientists explore origin and function of proteins.

In addition to the proteome draft map, researchers found 193 proteins, which are made by parts of the human genome that was considered to be ancient and non-functional.

''It will be interesting to compare our datasets to extend our understanding of the human proteome," said Gowda.

Some of the "missing proteins" were found in brain tissue samples, meaning that researchers are now one step close to finding cause and cure of several disorders including chronic meningitis and epilepsy.

''This is indeed a breakthrough research," said P Satish Chandra, director / Vice Chancellor of the National Institute of Mental Health and Neuro Sciences (NIMHANS).

Researchers at Bangalore collaborated with Akhilesh Pandey at The Johns Hopkins University to create the database for proteins. The team obtained samples from 30 different tissues and used molecular scissors to break the proteins into smaller bits called peptides. Researchers then used mass spectrometry to find proteins' relative abundance in the sample. The samples were derived from both adult and fetal tissues. Researchers found several proteins that were expressed only in early developmental stages.

''By generating a comprehensive human protein dataset, we have made it easier for other researchers to identify the proteins in their experiments," said Pandey in a press statement. "We believe our data will become the gold standard in the field, especially because they were all generated using uniform methods and analysis, and state-of-the-art machines."

The second, independent proteome draft was published by Bernhard Kuster of the Technische Universitat Munchen in Germany and his colleagues. Kuster and team catalogued about 92 percent of the estimated 19,629 proteins found in humans.

The team used mass spectrometry and in-memory computing to create the database. The team also found proteins that were coded by genes that were previously considered to be obsolete.

The finding creates as many questions as it answers. But what's certain is that despite sifting through genetic data for 11 years, scientists haven't figured out what a large portion of the genome does.

Both the research teams agree that the human genome is much more complex that previously assumed.