30 April 2006

Not junk after all

From IBM press releases page:

IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do. If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells.

“Our goal is to apply advanced computational techniques to analyze the workings of processes and systems, in this case the function of the human genome,” said Ajay Royyuru, head of the Computational Biology Center at IBM Research. “Using these tools, we’ve been able to shed new light on parts of the DNA that were traditionally thought of as not having a specific purpose. We believe the innovative application of technology can provide further understanding in the life sciences at large.”

The findings will be published in the next PNAS issue. Here is the abstract of the publication:

Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of {approx}22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For {approx}1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60–80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume {approx}40% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.

It is interesting that 98.5% of our genome is non-coding (meaning it does not encode functional proteins) and still, science does not leave it at that but keeps exploring and asking infinite questions about it, driven by simple reasoning: it is highly unlikable that the millions of years of evolution have left 98% of DNA that needs repairing, doubling, dragging to different sides of the cell in the process of replication, sifting through in the process of transcription etc., without any purpose for such a vast amount of nucleic acid. Finding a pattern in a chaos is usually a first step towards discovering a function.

IBM Research | Press Resources | IBM Discovery Could Shed New Light on Workings of the Human Genome

29 April 2006


SAR 11 is one of the most ubiquitous organisms on earth.
With it's 1.3 Mb genome, that was only recently sequenced and annotated, it is a smallest known bacteria (1/100th of the size of the average bacteria) and it thrives in the oligotrophic ocean. It's abundance is mind-boggling: 200,000 to 300,000 cells per milliliter! It is an aerobic heterotroph and only recently sucessfuly cultured in a lab. The comparative genomics is of particular interest, since it's genome can shed some additional light on the identity of the obligatory genes for survival in oligotrophic conditions, or if you like it, which of the genes were shed in the evolutionary reductive process.

This intriguing prokaryote is being researched at Stephen Giovannoni's lab in the Department of Microbiology at Oregon State University, where they had the honour of giving it its official proposed name: (Candidatus) Pelagibacter ubique.

I am presently writing a paper on the subject of "Adaptation of microorganisms to oligotrophic environment", so hopefully i will be able to write a comprehensive update on this topic soon.

28 April 2006

The Greatest Scientist

They say that it takes a good scientist to come up with the new theory, but only the great ones take the obvious things that are in fron tof our eyes and formulate it into a scientific theory.

Visit the Charles Darwin exhibit at the American Museum of Natural History. It may be a good starting point of a wonderful journey.


OK, here we go.

Of course i have heard of blogging and of course i had blogs and of course they ended after the third post. So what is different ?

I think that the difference is that now i would like to write about the topic that is my first love, my present time consumer and my future bread maker. Biology. If i have one advantage over a lot of people in my age group, it is the fact that i knew what i want to do with my life since about the age of five. It started with the chocolate bars that had animal stickers in them. Well, i used to throw away the chocolate. It continued with gathering water samples from puddles instead of splashing in them, bringing home lizards and insect, reading Brehm's Tierleben instead of Spiderman (well, in addition to...), watching the World of Survival every afternoon and wanting to become David Attenborough when i'm big.

It may sound nerdy to you, but i actually did not let go and proceeded to take biology as a major in high-school (together with computers) and am now at the end of my undergrad degree at Hebrew U in Jerusalem, majoring in biology and environmental sciences. I am in my last semester and are planning to continue next year into the graduate degree. During the years, my focus in biology has gotten smaller (molecular) and my love for the subject bigger. As someone smarter once wrote: "There is grandeur in this view of life"...

Here i am planning to write mainly about biology. Interesting stuff that i get exposed to in the course of my studies and my research, things i read on the net, new research and articles i stumble upon and interesting debates i read about on scientific blogs. There will be some personal stuff as well (only a little) and here and there computer/gadget/Internet related stuff.

Hope i will enjoy and persist in writing...