Thursday, June 30, 2016

Cancer Moonshot initiative on Cancer Genomics

You are aware that cancer is the second most deadly disease killing  thousands of people daily. As  cancer is a complex disease application of high throughput genomics methods opens up new avenues for understanding and treating the disease.  Cancer genomics programme is   moving to the next level because of the initiatives made by Cancer Moonshot Programme (Click here to read more about Cancer Moon Shot Programme). As part of the US-Cancer Moonshot and the US-President’s Precision Medicine Initiative, Foundation Medicine is more than doubling the total number of patients represented within the NCI's Genomic Data Commons (GDC), bringing its total to over 32,000 patients accumulated in just over a month.  At its launch in early June, the GDC already shared more than five petabytes of raw unprocessed genomic data from large research projects on nearly thirty tumor types from more than 14,000 patients, along with associated clinical data (e.g. clinical diagnosis, treatment history, survival data), creating a foundational system for broad sharing and analysis of cancer genomic data, which is critical for advancing the field of precision medicine and improving the care of cancer patients.

Tuesday, May 31, 2016

Why I want to discuss about climate change now ?:

There is a real possibility of Donald Trump becoming US president. He does not believe in climate change. Read his views below:

"Well, first of all, I’m not a believer in global warming. And I’m not a believer in man-made global warming. It could be warming, and it’s going to start to cool at some point. And you know, in the early, in the 1920s, people talked about global cooling. I don’t know if you know that or not. They thought the Earth was cooling. Now, it’s global warming. And actually, we’ve had times where the weather wasn’t working out, so they changed it to extreme weather, and they have all different names, you know, so that it fits the bill. But the problem we have, and if you look at our energy costs, and all of the things that we’re doing to solve a problem that I don’t think in any major fashion exists. I mean, Obama thinks it’s the number one problem of the world today. And I think it’s very low on the list. So I am not a believer, and I will, unless somebody can prove something to me, I believe there’s weather. I believe there’s change, and I believe it goes up and it goes down, and it goes up again. And it changes depending on years and centuries, but I am not a believer, and we have much bigger problems. You know, I talk about global warming. You know, to me, the worst global warming, and I mentioned this to you once before, is nuclear warming. That’s our global warming. That’s what I see, because we have incompetent people, and we have these rogue nations, and not even rogue nations anymore. You know, we had a case where Vladimir Putin about three months ago threw out the nuke word. And I never thought I’d hear that from a Russia. But he said they’d better, essentially, they’d better be careful, because you know, we are a nuclear nation. That was a hell of a statement for him to make. And that’s a statement that’s made because of a lack of respect."

If this is the belief of the future US president what happens to the Paris Agreement. He might scrap the agreement. If he becomes US president the world may be in trouble. I will post soon Scientific evidences available on current climate change

Friday, July 3, 2015

The 100,000 Genomes Project by UK

The project will sequence 100,000 genomes from around 70,000 people. Participants are NHS patients with a rare disease, plus their families, and patients with cancer.
The aim is to create a new genomic medicine service for the NHS – transforming the way people are cared for. Patients may be offered a diagnosis where there wasn’t one before. In time, there is the potential of new and more effective treatments.
The project will also enable new medical research. Combining genomic sequence data with medical records is a ground-breaking resource. Researchers will study how best to use genomics in healthcare and how best to interpret the data to help patients. The causes, diagnosis and treatment of disease will also be investigated. We also aim to kick-start a UK genomics industry. This is currently the largest national sequencing project of its kind in the world.

What is the US plan for next 5 years in Plant Genomics ?


Major objectives:

Objective 1: Develop a new generation of databases and tools to enable every step in the innovation chain from basic discovery to translation into practical application and widespread use.

Objective 2: Create a network of plant germplasm resources to meet the Nation’s research and breeding needs for the 21st century

Objective 3: Build tools to advance our understanding of plant biology and translate this knowledge into precision plant breeding for the development of sustainable systems for food, bioenergy, and industrial feedstock production

Objective 4: Empower the workforce to use a new generation of tools and resources

Objective 5: Build public-private partnerships to advance the translation of basic discoveries into practical application and support innovation in the practice of agriculture

Objective 6: Strengthen international partnerships to bring the benefits of new discoveries to all

Read the complete document for deatls

Wednesday, October 1, 2014

Next generation sequencing enables revisiting the concept of Non-collinear transcripts in higher Eukaryotas

An interesting class of transcripts called non-collinear transcripts was found recently when genomes were sequenced with NGS methods. They are chimeric RNAs that contain sequences from multiple non-collinear positions in the genome (some of them are mapped to different chromosomes are faraway positions in the same chromosome). Though genome rearrangements are said to behind their emergence no clear mechanism is known in eukaryotes.

Structural studies of RNAs in several species have revealed that the sequences that are ultimately joined together on the same mature transcript can be encoded in separately transcribed RNAs with multiple distinct genomic origins. Individual RNAs can be transcribed on separate chromosomes or on the same chromosome but with a different the genomic order from that found in the mature RNA or on the same chromosome but transcribed from different strands, or on the same chromosome but from different alleles. Similar phenomenon was known in lower organisms and the origin was due transplicing. For examples and more details read the following papers.

Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants

Assessing the hodgepodge of non-mapped reads in bacterial transcriptomes: real or artifactual RNA chimeras?

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Transcription-Mediated Chimeric RNAs in Prostate Cancer: Time to Revisit Old Hypothesis?

Friday, August 30, 2013

Why overexpressed proteins are toxic to E.coli ?

A majority of E. coli proteins when overexpressed inhibit its growth, but the reasons behind overexpression toxicity of proteins remain unknown. Understanding the mechanism of overexpression toxicity is important from evolutionary, biotechnological and possibly clinical perspectives. Here we study sequence and functional features of cytosolic proteins of E. coli associated with overexpression toxicity to understand its mechanism. We find that number of positively charged residues is significantly higher in proteins showing

Thursday, February 14, 2013

Breaking Discovery: Eighteen species of bacteria found in troposphere (between 8-15 km above the earth)

Microbes  are  said  to be in every part of earth including the hottest (under sea volcanoes)  and coldest (Polar regions) places of earth. What is being studied in Microbiology is those microbes which can be cultured. They constitute less than 1% of the total microbes in the earth.  Can you believe the news that  microbes exist  even in troposphere which is eight kilometres above the earth.  A recent study conducted by Scientists from School of Biology, School of Earth and Atmospheric Sciences, School of Civil and Environmental Engineering, School of Chemical and Biomolecular Engineering of  Georgia Institute of Technology at  Atlanta, USA and Chemistry and Dynamics Branch/Science Directorate, National