Monthly Archives: December 2012

Study explores the boundaries of embryonic development (eLife)

If all of the DNA in a human cell was stretched out, it would be about two meters long. The nucleus of a human cell, on the other hand, has a diameter of just 6 micrometers, more than 300,000 times smaller, so the DNA molecules that carry all the genetic information in the cell need to be carefully folded to fit inside the nucleus. Cells meet this challenge by combining their DNA molecules with proteins to form a compact and highly organized structure called chromatin. Packaging DNA into chromatin also reduces damage to it.

But what happens when the cell needs to express the genes carried by the DNA as proteins or other gene products? The answer is that the compact structure of chromatin relaxes and opens up, which allows the DNA to be transcribed into messenger RNA. Indeed, packing DNA into chromatin makes this process more reliable, thus ensuring that the cell only produces proteins and other gene products when it needs them. However, because cross-talk between neighboring genes could potentially disrupt or change gene expression patterns, cells evolved special elements called boundaries or insulators to stop this from happening. These boundary factors divide the chromosomes into subdomains that can function independently of each other.

Since the protein factors implicated in boundary function seemed to be active in all tissues and cell types, it was assumed for many years that these boundaries and the resulting chromatin domains were fixed. However, a number of recent studies have shown that boundary activity can be subject to regulation, and thus chromatin domains are dynamic structures that can be defined and redefined during development to alter patterns of gene expression.

New research from the laboratory of Paul Schedl at Princeton University has uncovered a new fruit fly boundary factor that, unlike previously characterized factors, is active only during a specific stage of development. The Elba factor is also unusual in that it is made of three different proteins, known as Elba1, Elba2, and Elba3, and all three must be present for it to bind to DNA. The lead author of the study was Tsutomo Aoki of the Princeton University Department of Molecular Biology. Aoki worked with co-authors Ali Sarkeshik and John Yates from the Scripps Research Institute in La Jolla, CA.

While Elba2 is present during most stages of development, the other two Elba proteins are only present during early embryonic development, so the boundary factor is only active in early embryos. In addition to revealing a new mechanism for controlling boundary activity as an organism develops, the studies of Aoki et al. provide further evidence that chromatin domains can be dynamic.

Aoki, Tsutomu, Ali Sarkeshik, John Yang, and Paul Schedl. Elba, a novel developmentally regulated chromatin boundary factor is a hetero-tripartite DNA binding complex. eLife 2012;1:e00171

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Article summary provided by eLife.

Truths we must tell ourselves to manage climate change (Vanderbilt Law Review)

Climate change is unwelcome news, and the best and worst outcomes consistent with current science are very different, says Princeton University’s Robert Socolow, professor of mechanical and aerospace engineering, in a new review article published in the Vanderbilt Law Review.  There are novel ways the environmental community, in its role as messenger, could tell the story about climate change using greater empathy and candor.  This essay, which was delivered as a keynote address at a symposium held Feb. 24, 2012 at the Vanderbilt Law School, addresses new ways to freshen the conversation.

The era of consciousness of climate change began in 1958 when Charles David Keeling began the first accurate measurements of carbon dioxide in the atmosphere. The seasonal oscillations were unexpected and the annual average has become a new index (the Keeling Curve) of global human impact.

Fifty-four years later, climate change negotiations in the United States and internationally are in paralysis. The current impasse has little social value and a “restart” button is needed. Such a button will be found when those already concerned about climate change become better at telling truths first to themselves and then to the general public. One can begin with acknowledgements that 1) climate change is unwelcome news, a challenge we would rather not have; and 2) the best and worst outcomes consistent with today’s climate change science are very different. Moreover, every nominal energy “solution” to climate change has a dark side and the solution’s proponents are not the ones to be counted upon to identify what can go wrong.

Accordingly, climate change is a problem of risk management requiring balancing the risks of disruption from climate change and the risks of disruption from mitigation and adaptation. Both public and private institutions need to find ways to overcome their reluctance to verify whether intended carbon reduction goals have actually occurred, so that progress can be accurately monitored and learning can occur. Individuals can be helped to become more aware of how their every-day activities create their carbon footprint. Population must reenter the conversation.

There are grounds for optimism. Science has discovered threats fairly early. Many helpful technologies are being developed and deployed. And, our moral compass is in working order, insisting that we care both for those alive today and for the collective future of our species.

Citation: Robert H. Socolow, “Truths We Must Tell Ourselves to Manage Climate Change.” Vanderbilt Law Review, Vol. 65, Number 6, pp. 1455-1478.

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Transition from individual to group behavior in bacteria (Journal of Bacteriology)

Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the bacteria known as Vibrio harveyi, two master “switches” of gene regulation, or transcription factors, coordinate the quorum-sensing response.The researchers found that one of the regulators, LuxR, acts as a sort of master switch that regulates quorum-sensing, while the other regulator, AphA, does the fine-tuning. Together the two regulators generate a precise pattern of activity as bacteria transition from acting as individuals to acting as a group.

Julia C. van Kessel, Steven T. Rutherford, Yi Shao, Alan F. Utria, and Bonnie L. Bassler. The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects
J. Bacteriol. published 30 November 2012, 10.1128/JB.01998-12

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New approach can rapidly estimate damage from earthquakes (Bulletin of the Seismological Society of America)

A new approach that can rapidly estimate damage to tall buildings following a large earthquake has been developed by researchers. The approach involves creating a database of building responses to typical earthquake-related ground motions. After an earthquake, an analysis of the ground motions can indicate what type of damage is likely to have occurred to nearby buildings. The results could be useful for emergency response decision making.

Swaminathan Krishnan, Emanuele Casarotti, Jim Goltz, Chen Ji, Dimitri Komatitsch, Ramses Mourhatch, Matthew Muto, John H. Shaw, Carl Tape, and Jeroen Tromp. Rapid Estimation of Damage to Tall Buildings Using Near Real‐Time Earthquake and Archived Structural Simulations. Bulletin of the Seismological Society of America. 2012; 102:2646-2666.

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