Cancer genetics: Nasty neighbourhood

Nature Genet. doi:10.1038/ng1596 (2005)

Tissue cells surrounding tumours can contain permanent changes to their genes that could encourage tumour development, say researchers. These ‘epigenetic’ changes take the form of chemical modifications to DNA and are passed on when cells divide.

A team led by Kornelia Polyak at the Dana-Farber Cancer Institute in Boston, Massachusetts, have developed a new way of screening the entire genome of a cell for epigenetic changes. They studied three kinds of cells in the tissues surrounding breast tumours and found alterations in all three. The changes resulted in abnormal gene expression in these cells. The findings suggest that epigenetic changes are involved in creating the abnormal tumour microenvironment thought to foster disease progression.

Immunology: Gut reaction

Cell 122, 107–118 (2005)

Lack of exposure to harmless bacteria has been blamed for the rising rates of allergic diseases, such as asthma, in industrialized nations. Support for this ‘hygiene hypothesis’ comes from a study that shows how a sugar produced by a gut bacterium directs the development of immune cells in animals.

A team led by Dennis Kasper of Harvard Medical School in Boston, Massachusetts, demonstrated that mice raised in a germ-free environment had several immune-system defects. These included unusually high proportions of immune cells called TH2 cells, whose abnormal activity is linked to allergies. Dosing such mice with the gut bacterium Bacteroides fragilis restored normal immune development. The team found this was due to a previously unknown kind of sugar called PSA that is made by the bacterium.

Materials science: Cracked it


Phys. Rev. Lett. 95, 025502 (2005)

When a piece of material breaks, what determines the shape of the resulting pieces? To find out, researchers from the National Centre for Scientific Research in Paris and the University of Manchester, UK, drove a cutting tip through a thin, brittle polymer film.

They say that, under certain conditions, the shape of the crack depends solely on the width of the cutting tool.It does not depend on the tool's speed, or on the width or thickness of the film. The researchers were also able reduce cracking behaviour to a simple set of geometrical rules, which they used to reproduce the fracture patterns created by several different shapes of cutting tool.

Medical microbiology: Secret sex life

Curr. Biol. 15, 1242–1248 (2005)

A fungus that causes life-threatening infections may have been having sex under researchers' noses. Until now, they thought it reproduced only asexually.

Aspergillus fumigatus can cause serious respiratory illness in people with weakened immune systems, and is a major cause of allergies. Paul Dyer from the University of Nottingham, UK, and his colleagues found that the A. fumigatus genome contains active genes very similar to those that other fungal species need for sex. They also discovered two different mating types, and evidence that genes can transfer between different populations. If the fungus has been hiding a furtive sex life, geneticists could perform breeding experiments to uncover the genes it uses to cause disease.

Synthetic biology: Close couple

Nature Chem. Biol. doi:10.1038/chembio719 (2005)

Scientists have designed a way to make proteins that works independently of the normal machinery in a bacterial cell. Jason Chin and Oliver Rackham of the Medical Research Council Laboratory of Molecular Biology in Cambridge, UK, have engineered two key components of this pathway in Escherichia coli.

The researchers altered both the ‘recipe’ for proteins, known as messenger RNA, and the molecular machines called ribosomes that turn this message into a protein.The engineered ribosomes can read only the altered RNA, and this RNA will not work in a normal ribosome. The researchers say these modified ribosome–RNA pairs will allow them to develop sophisticated ways of programming artificial processes inside living cells.

Neurobiology: Pore connections

Science doi:10.1126/science.1116270 (2005)

Voltage-dependent ion channels are complex protein structures that open and close, helping electrical signals to travel along nerves. They have sensors that can detect changes of a few hundredths of a volt and make the pore switch between closed and open states. But until now, no one knew for sure how the sensors work.

Roderick MacKinnon and his colleagues from New York's Rockefeller University have determined the first crystal structure of a mammalian channel in its natural state. They found that the voltage-sensing mechanism involves proteins that are quite independent of the pore itself. They also discovered that these sensing regions cross the membrane, which makes them unlike those in other kinds of channels. The team suggests ways in which the sensors could mechanically alter the shape of the pore.

Carbon chemistry: Get in the ring

J. Am. Chem. Soc. doi:10.1021/ja053202 (2005)

Japanese chemists have made the first stable molecular ring of silicon atoms. Various carbon-ring compounds, such as benzene, contain delocalized electrons that give rings extra stability, but no analogous molecules have been made for carbon's cousin, silicon.

The silicon ring contains three silicon atoms arranged in an equilateral triangle, carrying two delocalized electrons and an overall positive charge. Akira Sekiguchi and his fellow authors from the University of Tsukuba suggest that the rings could be stuck to metals to form catalysts. They now plan to generate all-silicon equivalents of benzene, and even buckminsterfullerene (C60).

Animal behaviour: Lighting the way

Credit: B. GUZNER

Biol. Lett. doi:10.1098/rsbl.2005.0334 (2005)

Locust swarms cover great distances, but avoid flying over large bodies of water. The insects (Schistocerca gregaria) use the polarized light reflected by the water to steer clear, according to Nadav Shashar and his colleagues at the Hebrew University in Israel.

Light waves reflected from flat surfaces such as water oscillate in a plane parallel to the surface, and some creatures — including locusts — can see this. Shashar's team caught locusts and tethered them above surfaces that reflect light in different ways. Sure enough, the insects tended to fly away from the strongly polarizing surfaces. The researchers hint that such materials could be developed to divert these destructive pests from crops.

Materials science: The hard stuff

Chem. Mater. doi:10.1021/cm0505392 (2005)

Polymers that conduct electricity have been toughened up by a team of chemists from the University of Manitoba in Winnipeg, Canada.

The development of polymer-based electronics has been limited by the poor heat-resistance and weakness of the materials. These properties are often due to the chemicals added to ‘dope’ the material, to boost conductivity. The alternative, linking parallel polymer molecules together to make them stronger, can block the current.

The team has made a polymer based on poly(anilineboronic acid) that is extremely hard and dopes itself. Heating the precursor polymer alters its structure and chemistry, leaving a charged boron atom that both makes the polymer a good conductor and links parallel chains.

Climate change: Here comes the rain

Geophys. Res. Lett. 32, L13701 (2005)

Climate change may heighten variation in precipitation from year to year, according to Filippo Giorgi and Xunqiang Bi at the Abdus Salam International Centre for Theoretical Physics in Trieste, Italy. Their region-based approach lends weight to previous work that suggests climate change could increase weather variability.

Giorgi and Bi divided the Earth's surface into a grid of regions, each 1 degree square. They used this grid system with 18 different computer models of twenty-first-century climate to see what differences were predicted over the years. In all regions the climate was warmer and the variability in the amount of precipitation from year to year increased significantly.

Journal club

Adam Summers University of California, Irvine

A biomechanist bones up on healing processes to work out why sharks are total softies.

Sharks, skates and stingrays have skeletons that are made entirely from a lightly calcified form of cartilage, but their ancestors had perfectly normal bone. A major question in my lab is why this should be. Maybe it's because cartilage is nearly neutrally buoyant, whereas bone is a real sinker. However, a recent finding has led us to think about the cost of repair too.

Although it is a structural material, cartilage is fundamentally different from bone. It lacks blood vessels and, in mammals, birds and amphibians at least, has virtually no ability to repair itself. Now it seems that cartilage in sharks lacks the ability to heal as well.

Doreen Ashhurst, of St George's Hospital Medical School in London, examined cuts in the fin supports of a shark (Scyliorhinus). She found absolutely no healing over six months (Ashhurst, D. E. Matrix Biol. 23, 15–22; 2004).

I find this very interesting. Ashhurst was testing whether a cartilage repair mechanism had evolved in an animal that relies heavily on the substance. What are the implications that it hasn't?

A human skeleton is shot through with thousands of microfractures in various stages of repair, with osteoclasts dissolving damaged bone and osteoblasts laying down fresh material. This remodelling saves us from developing significant fractures in bones that go through hundreds of loading cycles every day.

The skeletal elements of a constantly swimming shark may experience more than a billion cycles of loading over a long life. To survive, either the shark's skeleton must be heavily constructed so that it does not deform much on each loading cycle, or its cartilage must be remarkably resistant to fatigue.

My group now wonders whether the cost of continuously repairing the skeleton was a selective pressure that led cartilaginous fish to lose their bones.