Monthly Archives: September 2013

Sep. 9, 2013 A wide range of biologically inspired materials may now be possible by combining protein studies, materials science and RNA sequencing, according to an international team of researchers.

"Biological methods of synthesizing materials are not new," said Melik C. Demirel, professor of engineering science and mechanics, Penn State. "What is new is the application of these principles to produce unique materials."

The researchers looked at proteins because they are the building blocks of biological materials and also often control sequencing, growth and self-assembly. RNA produced from the DNA in the cells is the template for biological proteins. Materials science practices allow researchers to characterize all aspects of how a material functions. Combining these three approaches allows rapid characterization of natural materials and the translation of their molecular designs into useable, unique materials.

"One problem with finding suitable biomimetic materials is that most of the genomes of model organisms have not yet been sequenced," said Demirel who is also a member of the Materials Research Institute and Huck Institutes of Life Sciences, Penn State. "Also, the proteins that characterize these materials are notoriously difficult to solubilize and characterize."

The team, lead by Ali Miserez, assistant professor, School of Materials Science and Engineering, Nanyang Technological University, Singapore, looked at mollusk-derived tissues that had a wide range of high-performance properties including self-healing elastomeric membranes and protein-based polymers. They combined a variety of approaches including protein sequencing, amino acid composition and a complete RNA reference database for mass spectrometry analysis. They present their results in a recent issue of Nature Biotechnology.

The researchers looked at three model systems. The protein containing egg case membranes of a tropical marine snail are intriguing because they have unusual shock-absorbing qualities and elasticity. Investigation using the variety of methods showed this material has a coiled structure with crosslinking that absorbs energy. This information can be applied to biomimetic engineering of robust yet permeable coiled, protein-based membranes with precisely tailored mechanical properties.

The array of techniques applied toanalysis of a mussel foot showed that a species-to-species variation exists in mussel, including unusual variation in the protein. These variations suggest that protein engineering could produce a range of self-healing properties.

The final model used jumbo squid sucker ring teeth (SRT), grappling-hook-like structures used for predatory attacks. Analysis of the squid teeth showed nanotubular structure and strong polymers. While there was some similarity to silk and oyster shell matrix proteins, the protein was novel and the researchers named it Suckerin-39. Further analysis showed that Suckerin-39's structure allowed it to be reprocessed into a variety of shapes.

"While some biological materials have interesting properties, they cannot be reshaped or remolded because they do not soften upon heating," said Demirel. "The SRT is an elastomer, which is moldable, it is a thermoplastic and can be reshaped."

The materials properties of SRT do not change after heating and reshaping.

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Genome of elastomeric materials creates novel materials

Research team will look at medical and social consequences

Computational Biologist Steven Brenner will be part of an ambitious effort toassess whether large-scale gene sequencing aimed at detecting disorders and conditions can and should become a routine part of newborn testing.

Brenner, a professor in the Department of Plant & Microbial Biology at UC Berkeley, is part of a UC San Francisco team granted $6 million by the National Institutes of Health to identify the accuracy and feasibility of providing genetic sequencing as part of, or instead of, the current newborn screening that relies on biochemical changes in the blood. It also will assess what additional information would be useful to have at birth and the ethics and public interest in having such tests performed.

"Genome sequencing has the potential to reduce costs and improve theeffectiveness of newborn screening," Brenner said, allowing early intervention for infants and fundamental changes in the tehcnology for screening newborns.

The project has three broad goals:

The cost of genome sequencing has plummeted but the ethical and moral questions surrounding genetic testing loom large.

The first genome sequenced, about a decade ago, cost nearly $3 billion.Today scientists can sequence all of anindividual's genes for a few hundred dollars. The Brenner Lab, experts at computational biology, are at the forefront of this new area of science.

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Should genome sequencing for newborns be routine?

A fossilized bear bone, from which the genetic material was extracted. / Javier Trueba(MADRID SCIENTIFIC FILMS)

An international team that includes Spanish researchers has sequenced the mitochondrial genome (special DNA passed on exclusively by mothers) of bears who lived about 400,000 years ago in Atapuerca, near Burgos in northern Spain. This brings scientists closer to sequencing the entire genome of pre-Neanderthal humans who lived at the same time, and who hold clues about the evolution of our species.

The small mtDNA fragments were found inside samples of bear bones that were mixed in with hominid fossils at Sima de los Huesos (Pit of the Bones) at the Atapuerca site, which contains the world's largest collection of human remains from the Middle Pleistocene. Until now, the oldest samples of DNA recovered in temperate areas - not frozen at high altitudes - were between 100,000 and 120,000 years old.

The breakthrough could have significant implications for human paleontology.

"Let us hope that the methodology that we are presenting here will help recover ancient DNA sequences from other organisms of the Middle Pleistocene. The fossils of Sima de los Huesos are the target of these efforts," write Jesse Dabney and his colleagues in Proceedings of the National Academy of Sciences (PNAS), which this week publishes the entire mitochondrial genome of those early cave inhabitants.

"Yes, of course I am optimistic about the possibility of obtaining DNA from human fossils at the pit; if it is there in the bear bones, it can be there in the human bones, which are contemporary to the latter," says Juan Luis Arsuaga, co-director of the Atapuerca site and one of the authors of the new study.

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Bear genome at Atapuerca paves way for earliest hominid sequencing at site