April 27th, 2006



в некодирующей части человеческого генома обнаружены скрытые паттерны

Junk DNA: a team from IBM has identified patterns, or "motifs", that were found both in the junk areas of the genome and those which coded for proteins


Lead author Isidore Rigoutsos and colleagues from IBM's Thomas J Watson Research Center used a mathematical tool known as pattern discovery to tease out patterns in the genome. This technique is often used to mine useful information from very large repositories of data in the worlds of business and science.

Dr Rigoutsos said his team's work suggested, "a connection between a vast area of the genome we didn't think was functional with the part of the genome we knew was functional".
The paper in PNAS suggests that the actual positioning of the motifs is associated with small RNA molecules that are involved with a process called post-transcriptional gene silencing (PTGS).
"These regions may indeed contain structure that we haven't seen before," said Dr Rigoutsos.
"If indeed one of them corresponds to an active element that is involved in some kind of process, then the extent of cell process regulation that actually takes place is way beyond anything we have seen in the last decade."

Original paper: PNAS, April 2006
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

такая картина ожидалась многими, кто не спешил верить в 96% мусора...Можно сделать предсказание в longBets : будущее применение мат. и стат. методов вместе с развитием dev.bio позволит обнаружить логику (правила) в 'некодирующих' регионах и, возможно, нам откроется иерархия кодов...


о регуляции регуляторов...

Science, 21 April 2006
Gene-Suppressing Proteins Reveal Secrets of Stem Cells
According to papers in Cell and Nature this week, key guardians of stemness are molecules called polycomb group proteins. A team from the Massachusetts Institute of Technology (MIT) and the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, reports that these proteins act in concert with others to repress most of the regulator genes whose proteins turn on key developmental genes. This keeps the ES cell in an undifferentiated state.

how a web of chromosome interaction can help to explain gene regulation in humans
Gene regulation is a major issue in biology - how are different genes activated in different tissues or at different times in life, and how and which genes interact with each other? A major breakthrough in the understanding of this issue is about to be published in the scientific journal PLoS Biology by Miguel R. Branco and Ana Pombo...The two scientists show that chromosomes in the nucleus of metabolically active cells are largely intermingled, and that this physical contact is associated with their gene activity. The researchers propose that chromosomes exist in an intricate network of interactions, which are specific for each cell type, and which result in interactions between genes of different chromosomes.

PLoS Biology, May 2006
Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations

см. также про внутриклеточное управление движением хромосом в ядре посредством молекулярных моторов


Our Universe: A Quantum Loop

While Abhay Ashtekar and his colleagues may not have come with a completely new theory, what they have done is create a systematic way, through quantum equations, to look back in time to the birth of our current universe.

“There are two classical branches of the universe connected by a quantum bridge. This connects the former collapse with the current expansion.”

Ashtekar’s team from Pennsylvania State University’s Institute for Gravitational Physics and Geometry published a Letter in Physical Review Letters on April 12th, detailing what was found, and shedding a little more light on what actually happened at the time the universe began expanding.
“The idea of a bounce has been around for a while,” Ashtekar explains, “and it has been looked at in many contexts. One of them is String Theory.” He continues: “The pre-Big Bang cosmology considered the idea that a branch of the universe existed before the Big Bang, and in the Ekpyrotic scenario, a `brane’ collides with another `brane,’ causing a bounce.”

The pre-universe collapses-in on itself. However, a new kind of repulsive force comes into play because of the quantum properties of the geometry itself.

“No matter how heavy, how much mass,” says Ashtekar, “this repulsive force still wins out. When the universe reached a point of high Planck density, the repulsive force bounced it out.” Ashtekar’s team created the first detailed calculations that show classical behavior in the universe before the epoch of the Big Bang. “This is the time when quantum physics and relativity must be combined, and at this point the new physics causes a Big Bounce. And we find the equations that tell us that before this Big Bounce, there was a classical universe.”

см. Абэй Аштекар и петлевая квантовая гравитация