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Saturday, April 3, 2010

Joining forces against TB

A partnership involving the US Food and Drug Administration may speed up delivery of new tuberculosis drug combinations, says Priya Shetty.

New TB drugs are desperately needed. The existing treatment is a cocktail of drugs that must be taken over 6–8 months. Often, one of the biggest challenges facing healthcare professionals is simply ensuring that their patients finish the course of treatment. Full-Text Article: http://scidev.net/en/health/hiv-aids/opinions/biomed-analysis-joining-forces-against-tb.html

TB GO on the GO

The TB GO team has moved to onsite mode. A nerve centre has started functioning at the CSIR IGIB facility at Naraina. Yes, the same centre which sequenced human genome and the one which hosts the IT infrastructure of OSDD. Amidst the hum of the machines and scientists in their coats, a bunch of Connect to Decoders has moved in today to Dr. Vinod Scaria’s lab.

It is indeed an interesting lab. One which any bio-informatician would like to be part of. A series of servers lined up in a state of the art server room gives out a regular hum and lights go on and on. Few rooms away are state of the art sequencing machines. Adjacent to the server room separated by a glass, is a row of computers.

As you walk in a bunch of Connect to Decoders are already infront of the screens and immersed in working. They had just reached New Delhi railway station two hours ago. This is what is called hitting the ground running.

In the afternoon they had an unusual visitor. Jean Marie from UK who is writing a book on innovation in China, India, South Africa and Brazil was wanting to know about OSDD. What better way to know about OSDD but to speak to Connect to Decoders.

The GO team is here to do the last bit of QC. Or, may be, they will throw a surprise when you meet them. You don’t get a bunch of bright young minds and expect nothing, right?

Friday, April 2, 2010

To Tokyo via Ghaziabad

The IPW team is working extra time to finish the QC on the IPW data. The team is led by Dr. Anshu who is at the White Board with plans, sketched and schedules. The team is gung ho and literally burns midnight oil. It is not sure if burning midnight oil is the correct term to use as they go to sleep only at 3.00 AM in the morning. Few days back they had the excitement of seeing the first network, now the effort is to make it as comprehensive and as meaningful as possible. They are online with Tokyo on all the days.
They had the Chief Mentor calling on them to see the progress. They were on skype with SBI Japan. Dr. Kitano joined from Tokyo. Discussions were on plans, networks, pathways and how to develop production level data to be readied for mapathon when the rest of the team comes in on 9th. Later the network map generated on Cell designer was seen by the Chief Mentor. Dr. Brahmachari was thrilled to be with the Connect to Decoders. Questions started flowing on all directions. What is critical or not… what is the function of the pathway, which is distinctive which is not…. And Dr. Brahmachari was most impressed by the young Connect to Decoders.
Later Dr. Nagasuma joined from IISc Bangalore on the protein structure annotation progress.
The air is abuzz with activity…technology is in full flow
You can expect an exciting scientific exploration during the onsite phase... Gears up, folks!

Wednesday, March 31, 2010

First Network

It is exciting and emotional to see the First Network that the IPW Team generated using Cell Designer for the first set of quality checked data !!! Samik from the Systems Biology Institute. Japan, has been interacting with the Team working from Delhi through Skype calls. Today we also interacted with The Chief Mentor and Project Director of OSDD through Skype and had interesting discussions on network analysis. Watch out for more...we are at it.

Annotating the Tb Glycome

Glycome… the fancy and less friendly cousin of the proteome and the genome is an interesting component of any organism. Comprising of the enzymes that add, lengthen, reduce, modify and change sugar residues in a protein or lipid, they actually comprise that “unknown” factor that the scientists often do not dare to look into. Glycans are difficult to study : with 9 sugars able to branch in endless possibilities and form zillions of structures, having no template driven synthesis mechanism and extremely challenging to sequence. But still, glycosylation is the most prevalent post-translational modification, often being responsible for cell-cell interaction, infection development, antigen-antibody mediation and reproductive biology to mention a few and hence cannot be disregarded. However, though their role in infection development is acknowledged, very little experimental research is actually available on it. Prokaryotic glycosylation came into the focus of scientific research only in 2002 when a N-glycosylation equivalent pathway was discovered in Campylobacter jejuni. Research has been ongoing since then to identify these genes in other bacteria.

The GlycoMtb team of the OSDD C2D initiative, focuses on the Mtb glycome, a very poorly characterized sector of the Tb genome. The existing genome annotation showed only 100 known genes for glycosylation in Mtb. But clearly, there has to be more…! In an organism that has the most complicated of the cell wall structure that comprises of glycolipids, an organism that fools the host defence mechanism and develops the deadliest of the diseases in humans definitely has more than 100 odd genes for the glycosylation pathway. Armed with this belief, the GlycoMtb team used a 2 pronged approach. The first phase was to look for homologues of bacterial glycan modifying enzymes in Mycobacterium. This gave an important lead… the answer to the genes responsible for glycosylation lay in the 1500 odd genes annotated as “hypothetical protein/conserved hypothetical protein/conserved membrane protein”. Hence bagan the long journey amidst the amino acid sequences, looking for sequence similarity, pattern matches and secondary structure matches. The team finally emerged 2 months later with a full functional prediction of the unnamed proteins…. Reducing the number of "proteins with unknown function" from 1500 to 270. As of now we have about ~400 genes which may be glycan modifying and maybe another hundred or so which are glycoproteins. This phenomenal task has only been possible due to the “nothing is impossible” belief of the team members , essentially made up of master’s students across the country.

The team is still at work incessantly, trying to make a more comprehensive list of the enzymes and proteins which they feel holds the key to a lot of unanswered questions in Mtb infection and hoping to release the data in the upcoming C2D conference in April 2010.

Tuesday, March 30, 2010

BBC World News on OSDD

Tuberculosis is one of the world's oldest diseases. It's been so good at surviving through the millennia that today one third of the world's population carries it. As certain strains begin to develop resistance against the commonly-used drugs the hunt is on for a new treatment – a hunt that has taken more than thirty years without success. Angela Saini reports from India - which has a fifth of the world's TB cases – on how a new online project is hoping that by pooling the knowledge of the world’s best scientists they might come up with the answer.


Listen to the Clip: http://www.bbc.co.uk/iplayer/console/p006wgns

More on the clip at Angela Saini's Blog : The Hunt for the new TB Drug

Sunday, March 28, 2010

C2D Programme Update

We have just updated the Programme for C2D10. We have added a few more speakers and workshops that we feel the C2D team would enjoy.

The Programme details are also available at the C2D10 Website at URL: http://c2d10.osdd.net/programme

C2D Onsite Phase Begins

At the Ops Room
Away from the buzz of Delhi, nestled among green trees frequented by birds, is CSIR's Human Resources Development Centre at Ghaziabad. HRDC is having a bunch of unusual group. Usually frequented by scientists and leaders of CSIR, is now the hub of Connect to Decode activity. Dr. Anshu Bhardwaj has quietly started the onsite phase of Pathway Annotation project. Her handpicked team leaders are quietly doing the Quality Control (QC) check of the data annotated by the team.

As you walk into the room, you get the sense of walking into the Ops Room of a major military operation. The air is tense. Hardly any words are spoken. Work is brisk. Fingers work on the key boards like that of a skilled tabla player. You might have heard of power play in cricket. This team has devised power sessions which last for an hour. After each power session there is a lean hour, again a power session...and on and on they go till late into the night. Dr. Anshu has to drag out her team for lunch and coffee. Except on one occasion- if a peacock is dancing with full bloom, the team takes a break to peek a look and you can see Rohit running with his camera. But sensitive as they are the peacocks shy of their dance very soon and the team is back on their keyboards with their fingers dancing with double vigour.

Some photos…