Tag Archives: Genomics

Possibility of Ideal Intestinal Remedy

I’m not able to keep intestinal condition without remedy which is prepared by Lactobacillus, Bifidobacterium, Lactococcus, and others. Eating yogurt is also okay for this purpose, ad personam I prefer to take these bacterial tablets and believe more effects. However, many people know these effects of current intestinal remedies are mild not fast-acting properties.

Several reports mentioned that intestinal bacterial flora and its regulation were not simple. It is starting discussion that natural immunity may regulate intestinal flora; e.g. antibacterial peptide α-defensins which is secreted from paneth cells on small-intestinal epithelium could regulate flora distribution (Salzman et al., 2010; Matsuda et al., 2011). By contrary, very simple strategy is reported as following: Clostridium difficile brings bad diarrhea that was resistant to antibiotic. Van Nood and co-workers (2013) injected healthy person’s feces into patient’s guts, and its curative effect was so good surprisingly, but we cannot call it a remedy!

Two NGS platforms, GS FLX/Junior and MiSeq, can perform distributional analysis via deep sequencing of 16S-rRNA amplicons. But it is still difficult for both platforms to do metagenome assembling for getting whole gene information in flora, because their read length is not long enough to make reliable contigs without chimeras between different bacteria one another. Therefore I strongly expect that super long read platforms including PacBio RS series and coming nano-pore technologies will break current limitations and will contribute to develop ideal intestinal remedy for my instable stomach.

Tip: Inside The Wellcome Trust Sanger Institute

Do you know the blog of the Wellcome Trust Sanger Institute?

The Wellcome Trust Sanger Institute is one of the leading genomic research centres in Europe and a leader in the Human Genome Project. Within their blog they are talking about the role of genetics in health and disease by using the latest genomic and genetic techniques.

Read more at http://sangerinstitute.wordpress.com/

Think Big: American Gut Project Based On NGS

Scientists estimate that the cells of our bodies are outnumbered 10 to 1 by bacterial cells which live in or on our body.  A previous blog has already pointed out the impact of this fact on sequencing the corresponding host genomes. On the other hand, microbiomes have the potential to play an important role as diagnostic markers, or opening up new ways of treating diseases, such as personalized medicine.

However, we are just beginning to understand the complex relationships of this “social network”, as the Scientific American has called it. The most complex bacterial community within the human body resides inside the gut. In order to obtain a deeper understanding of the bacterial communities of the human gut, there have been several attempts of sequencing the gut microbiomes of larger groups of individuals, such as projects by Arumugam et al., Yatsunenko et al or Schloissnig et al. However, so far, the number of individuals which were analyzed was relatively small (up to several hundreds).

A group of US scientists have now started the “American Gut Project“.  As reported by Genome Web News, this project is planned as a crowd-sourcing study of 10.000 or more individuals in the US. Since this study is part of the “American Food Project”, it will mainly focus on gut microbiome patterns in relation to diet, age and lifestyle. People who would like to participate in this study need to sign up via a website and donate $99. This money will be used to cover a significant part of the cost of the study. In return, participants will receive a taxonomic profile of their gut microbiome.

The analysis itself will be based on 16S sequencing. For part of the samples, additional analyses such as sequencing the complete metagenomes and long term surveys are planned. No doubt, this study will clearly provide us with a huge data set. However, this data set will be highly complex. Also, it still needs to be brought in context with data from other projects.  To my opinion, interpretation of the data still remains the hardest part. Or, as project organizer Jeff Leach has put it in an interview with Genome Web Daily News: “We don’t expect to be able to address some questions, but because of the size of the sample and because of the broad patterns we expect to see in diet and lifestyle, we think some stuff will fall out.”

NGS goes to the Big Apple

Six floors for Next Generation Sequencing in the middle of Manhatten – this is going to be exiting. Listen to the interview from Bio-IT World with Nancy Kelly, founding executive director of the New York Genome Center.

The singing mouse

Next Generation Sequencing (NGS) is transforming today’s genomic research and is used in numerous applied areas from clinical diagnostics to academic research. In Texas USA, Dr. Steven Phelps and his research team recently used NGS sequencing to discover a gene which allows mice to communicate by singing a song. I have to admit it sounds more like screaming than singing to me. But Phelps and his team found out that a gene called FOXP2 is responsible for this way of communication.

Phelps’ uses next-generation sequencing to decipher how FOXP2 interacts with DNA to regulate the function of other genes. The process involves reading tiny fragments of overlapping DNA so that the entire sequence can be deduced. It is a procedure that generates massive amount of data that only the processing power of a supercomputer can handle, said O’Connell (Source: www.tacc.utexas.edu). So data handling & storage is still one of the biggest challenges when performing Next Generation Sequencing projects. But now take the chance an listen to the song of this little mouse.

The Genomic Landscape 2012

Eric Green is talking about the genomic landscape. Please enjoy the great presentation – starting at min 6.00.

Genomics is More Than Research

During my routine scan through the news on GenomeWeb I encountered an interesting article from Christie Rizk Knowledge of Genome Can Both Simplify and Complicate Knowledge of Self. This article is about the book My Beautiful Genome from Lone Frank who is a scientific journalist with Ph.D. in neurobiology.

On the homepage of Lone Frank you can find a sneak peek and these 6 pages contain already so many insights into human thinking and facts about the genome, that you really start thinking about your genome. Would you really like to know, if you had a hereditary disease? On the other hand it might be an extremely happy moment in your life when you learn that you don’t have a specific gene variant that is present in one of your parent’s genome.

I totally agree that we need research on the genome, since we need to know more about genes and their impact on our lives. In your private life your personal genome can provide information whether there is increased risk for a selection of hereditary diseases. Despite that it is still your decision and responsibility whether and to what extent you like to work with your personal data, isn’t it?

Knowing one’s genome may however also a fatal decision. What, if you find out a predisposition for a disease that cannot be treated?  This may even cause severe psychological problems .  In this context it is frightening that  some companies try to make money with dubious tests that have no scientific justification. What do you think?

Genomics for Beginners

Watch that great genomics tutorial. Find out what genomics means and how it relates to DNA and genetics. The video tells about the correlation between genomics and human health, our environment and our knowledge about how we fit into our world.

Next Generation Sequencing: Is There New Hope For Patients With Rare Diseases?

Some new studies published online in Science Translational Medicine  ( Sirota et al. > and Dudley et al. > ) demonstrate the potential of genomics to find new applications for existing drugs ( GenomeWeb >). They detected 53 significant drug-disease interactions. In one case they could find evidence that the ulcer drug cimetidine might be effective against lung cancer.

This gives new hope for effective treatment of rare diseases, where new potential orphan drugs are not available.