Recently in Biological physics Category

The point defect in diamond known as the NV center—a nitrogen atom substituted for a carbon atom and adjacent lattice vacancy—has become a promising ingredient in recent efforts to develop atomic-scale sensors. When optically excited, the defect exhibits stable fluorescence, even in a crystal as small as 5 nm. And its ground state is magnetically sensitive—the spin 0 level is separated from degenerate spin ±1 levels by a microwave transition of 2.9 GHz. That sensitivity allows one to detect weak magnetic fields by observing the quantum spin state, which can be manipulated by microwave pulses and then read out optically by monitoring the fluorescence intensity. (The intensity depends on which of the three spin states is populated.) Researchers led by the University of Melbourne’s Lloyd Hollenberg have now performed such magnetic resonance experiments on individual nanodiamonds placed inside human cells. The quantum spin levels of the defects acted both as local magnetometers and as fingerprints to spectrally distinguish each nanodiamond in the complicated cell environment. Using a confocal microscope, the researchers were able to identify and track at nanometer precision individual NV centers in the cells from the optical emission (red). They were also able to measure the coherence time of the spin states; that work sets the stage for sensing the cells’ local magnetic fluctuations in response to, for example, the transport of charge through cell membrane ion channels, which are important drug targets. (L. P. McGuinness et al., Nat. Nanotechnol., in press, doi:10.1038/nnano.2011.64.)—R. Mark Wilson

To gather clues about the structure of a protein, DNA, or other chain-like biomolecule, researchers can tag it with two fluorescent dyes. In what's known as fluorescence resonance energy transfer (FRET), the excitation of one dye, the donor, can cause a nearby partner, the acceptor, to also fluoresce. The resulting two-color burst of photons hints at the biomolecule's shape: The larger the contribution of the acceptor to the total fluorescence, the closer the dyes. Now, two groups have paired single-molecule-resolution FRET with microfluidics to shed light on complex biophysical phenomena. Ashok Deniz (Scripps Research Institute, La Jolla, California), Alex Groisman (University of California, San Diego), and colleagues used a novel microfluidic design to quickly initiate folding of a tagged protein and then track the time evolution of the donor–acceptor distances. Their experiment revealed the three-step process, illustrated here, by which the protein α-synuclein folds from its intrinsic disordered state into an extended helix. Another group of researchers led by Shimon Weiss (UCLA) and Stephen Quake (Stanford University) devised a microscale network of flow channels, valves, and pumps to facilitate high-throughput FRET experiments. The team used the device to investigate effects of chemical environment on bacterial RNA transcription, which could be detected as changes in fluorescence when tagged DNA strands hybridized with matching RNA strands. (Y. Gambin et al., Nat. Methods 8, 239, 2011; S. Kim et al., Nat. Methods 8, 242, 2011.)—Ashley G. Smart

X-ray crystallography is remarkably successful at yielding atomic-resolution structures of proteins and other biological molecules. But that success relies on growing macroscopic crystals. Unfortunately, some molecules crystallize with difficulty or not at all. A decade ago, researchers predicted that the femtosecond pulses from an x-ray laser would be short enough and intense enough to produce a useful diffraction pattern from an uncrystallized biomolecular cluster before vaporizing it. An international collaboration of more than 80 scientists has now used SLAC’s Linac Coherent Light Source free-electron laser to perform two proof-of-concept demonstrations of the feat. In one study, the researchers squirted a suspension of nanocrystals (the photosynthetic protein photosystem I) across the 1.8-keV x-ray beam, recorded the two-dimensional diffraction pattern each time a crystal intersected the beam, and then combined 15 000 single-crystal snapshots to form the 3D projection shown here. From the data, the team reconstructed the protein’s structure at the near-atomic resolution of 8.5 Å, just over the x-ray wavelength. In the second study, the team injected an aerosol stream of 0.45-µm-diameter noncrystalline mimivirus particles across the beam. Thanks to the beam intensity—nearly 10¹³ photons per pulse—the collaboration was able to transform the diffraction pattern of a single virus particle into a real-space projection of its interior, though at the more modest resolution of 32 nm. The studies represent a step toward making molecular movies at atom-by-atom detail using harder and shorter pulses. (H. N. Chapman et al., Nature 470, 73, 2011; M. M. Seibert et al., Nature 470, 78, 2011.)—R. Mark Wilson

Irving Epstein and his coworkers at Brandeis University in Waltham, Massachusetts, have shown that a chemical mechanism for producing patterns in two dimensions also works in three. Proposed in 1952 by Alan Turing, the mechanism relies on the competition between a slow-diffusing chemical that activates a reaction and a fast-diffusing chemical that inhibits the reaction. Nudging the reaction–diffusion system into a metastable state yields stable stripes, spots, and other periodic patterns. Turing's analysis and its subsequent experimental confirmation was for two-dimensional systems. Although computer simulations suggest the mechanism also operates in 3D, proving it does so in the lab is challenging: The extra spatial dimension makes it difficult to see patterns inside the medium. To meet that challenge, the Brandeis team used optical tomography to view a medium made up of aqueous droplets embedded in oil. Turing's model doesn't ordinarily apply to such an inhomogeneous medium. However, by coating the droplets with a surfactant, the team ensured that the slow-diffusing activator and fast-diffusing inhibitor leaked in and out at rates that sustained pattern formation on scales larger than the droplets themselves. To monitor the system, the team rotated the reaction vessel (a quartz cylinder) in front of a camera that took a sequence of 2D images. Tomographic reconstruction of the system under different initial conditions revealed a gallery of structures, including the labyrinthine worms shown here. Epstein anticipates that the 3D version of Turing's model may explain the formation of some biological patterns, such as the process by which Hydra regrows its tentacle-tipped head after decapitation. (T. Bánsági, V. K. Vanag, I. R. Epstein, Science, in press.)—Charles Day

When imaging, monitoring, or stimulating samples in a scattering medium, even the most powerful optical microscopes and probes are hindered by the diffusion limit, the length scale beyond which the incident light uncontrollably scatters. To overcome that limit, some techniques focus the wavefront as it propagates through the sample; others iteratively shape it to amplify the target signal. Lihong Wang and colleagues at Washington University in St. Louis have developed a new approach that combines time reversal with ultrasound, whose waves scatter weakly in biological tissue, to focus light to a controllable position. (For an introduction to multiwave imaging, see the article by Mathias Fink and Mickael Tanter in Physics Today, February 2010, page 28.) In the team's setup, laser light, frequency-shifted by two acousto-optic modulators in series, entered the sample medium, where the diffused light was further modulated by an ultrasonic wave tuned to the frequency shift. The interaction between the light and the ultrasound produced a virtual point source within the sample. From a holographic record of the modulated diffused light, the researchers generated a time-reversed trajectory that produced optical focusing at the virtual source location. The new technique, known as time-reversed ultrasonically encoded (TRUE) optical focusing, generated a noticeably higher contrast for objects inside a slab of synthetic biological tissue than was attained by conventional ultrasound-modulated optical tomography, which cannot focus light. (X. Xu, H. Liu, L. V. Wang, Nat. Photonics, in press, doi: 10.1038/nphoton.2010.306M.)—Jermey N. A. Matthews

The chemistry of life is complicated. Gene expression, in which information is transcribed from DNA to messenger RNA and then translated to produce a protein, involves more than 100 different molecules. Gaining a quantitative understanding of the process through observation of living cells is a daunting challenge. Now, Vincent Noireaux (University of Minnesota), Roy Bar-Ziv (Weizmann Institute of Science in Israel), and colleagues have used a cell-free system to carry out a complete gene-expression reaction, and they’ve developed a simple model of the reaction dynamics. Cell-free protein synthesis itself is not new; it’s been used for 15–20 years to produce proteins for research and medicine. Typical cell-free systems, which are available commercially, are therefore optimized to produce a lot of protein quickly rather than to reproduce reactions as they occur in vivo. The systems combine molecules from different organisms, and they don’t allow control over biologically important reactions such as mRNA inactivation and protein degradation. Noireaux and his student Jonghyeon Shin developed their own cell-free system, using molecules only from Escherichia coli bacteria and including enzymes for inactivation and degradation. Bar-Ziv and his student Eyal Karzbrun carried out experiments to determine how each component’s concentration affects the amount of protein produced. They found that they could describe the system’s main features by treating each process—transcription, translation, inactivation, and degradation—as if it were catalyzed by a single enzyme. The researchers’ next step is to extend the system to study more complicated processes, such as in circuits of several genes that affect one another’s expression. (E. Karzbrun et al., Phys. Rev. Lett., in press.)—Johanna Miller

If given ample food, bacteria proliferate exponentially. If given little or low-quality food, bacteria proliferate sluggishly. Behind that adjustable growth lies a complex web of interconnected molecular pathways, the elucidation of which is a major goal in biology. But, as Terence Hwa of the University of California, San Diego, and his collaborators demonstrate, you can accurately model the outcome of those complex reactions without knowing the details. Hwa and his colleagues based their model on experiments that revealed the relationships between proliferation rate, nutrient quality, and the ratio of RNA to protein inside the bacteria. That ratio, which is straightforward to measure, is significant because all proteins are made by RNA-rich ribosomes: The more ribosomes in a cell, the faster the cell can grow and multiply. The mathematical relations that emerged from the UCSD team's analysis are simple and linear, and they reflect how cells allocate resources. In a nutrient-rich environment, the cell can afford to synthesize ribosomes at the expense of metabolic proteins, but when nutrients are scarce, metabolic proteins are synthesized at the expense of ribosomes. The balance between the two classes of biomolecule determines the growth rate. To test their model over a broad range of parameter space, Hwa and his colleagues observed two kinds of mutant: one whose ribosomes translate more slowly and one that overproduces a useless protein. The model passed. Hwa likens it to Ohm's law, which enables electrical engineers to design circuits without knowing the band theory of electrical conduction. Given that mutant bacteria are used to make drugs and other useful chemicals, the UCSD model could prove similarly useful. (M. Scott et al., Science 330, 1099, 2010.)—Charles Day

The bacterium Shewanella oneidensis enjoys a unique respiratory versatility: not only can it use oxygen as a terminal electron acceptor, as do humans, but it can also transfer electrons to extracellular minerals such as iron oxides. Researchers hope to use that flow of electrons to, say, power microbial fuel cells or remediate soil contaminants, but they remain conflicted as to how the feat is carried out. Two theories have emerged: that microbes secrete shuttle molecules that diffuse to a metal’s surface, deposit electrons, and then return to start the process anew; and that on contacting a suitable metal, they pass electrons directly across the cell membrane. A team led by Charles Lieber (Harvard University) and Bradley Ringeisen (US Naval Research Laboratory) has produced new evidence in favor of the shuttle hypothesis. The researchers conducted a tiny fuel cell experiment with two types of nanoelectrodes—one exposed via openings too small for microbes to access, shown in the figure, and the other with large, accessible openings. Both yielded roughly equal current. Meanwhile, experiments by Mohamed El-Naggar (University of Southern California), Yuri Gorby (J. Craig Venter Institute), and colleagues support the direct contact mechanism. Applying voltage drops along the bacteria’s pili—long filament-like appendages that might attach to metal surfaces—they observed lengthwise conductivities sufficient to keep pace with bacterial respiration. It’s possible, maintain both teams, that microbes can choose either strategy based on the demands of their environment; the groups are now collaborating to find out. (X. Jiang et al., Proc. Natl. Acad. Sci. USA, 107, 16806, 2010; M. Y. El-Naggar et al., Proc. Natl. Acad. Sci. USA, 107, 18127, 2010.)—Ashley G. Smart

Like their optical-tweezer cousins, magnetic tweezers have become a standard tool for stretching individual biological molecules to gain insight into their physical properties and behavior. Magnetic tweezers (and optical ones, too) can also apply torques to rotate or twist specimens. Last year, Sean Sun of the Johns Hopkins University and colleagues developed a technique to control and measure the applied torque with magnetic tweezers. In their approach a biomolecule, such as DNA, was connected to the middle of a 2-µm-long nanorod that was magnetically latched at one end to a superparamagnetic bead. In a dipole magnetic field, the bead held the nanorod and the top of the molecule in place while the experimenters introduced a controlled amount of twist by rotating the substrate bound to the molecule's other end. Nynke Dekker and her coworkers at the Delft University of Technology have now presented a new take on magnetic torque tweezers, this time using standard spherical beads. A nonmagnetic bead 1 µm in diameter served as a landmark on the 2.8-µm-diameter superparamagnetic bead to which it was attached (a third, nonmagnetic reference bead corrected for mechanical drift). The larger bead was tethered to a substrate by a single DNA molecule, and the beads were placed in a slightly asymmetric dipole magnetic field. Rotating the magnet twisted the DNA, and by monitoring the beads' orientation the team could extract the DNA's torsional stiffness and the torque. With their tweezer setup, Dekker and colleagues could document torque-induced twisting, buckling, and denaturing of DNA under a wide range of torques and stretching forces and could study protein–DNA interactions. (J. Lipfert et al., Nat. Meth., in press, doi:10.1038/nmeth.1520.)—Richard J. Fitzgerald

The public-health and biosecurity communities need biosensors that are sensitive, operate in real time, and can be easily deployed. Many approaches are being pursued, including one by a group from Lawrence Livermore National Laboratory that uses a photonic crystal (PC) slab connected to two waveguides. The idea is for viruses or other tiny pathogens to randomly infiltrate the pores of a silicon PC, whose optical properties—specifically, the in-plane transmission spectrum's band edge—change accordingly. First, the researchers used simulations to determine a PC geometry suitable for a specific virus, vaccinia, and for their laser's wavelength. They then fabricated an appropriate 17 × 17 array of 280-nm pores and exposed it to a flux of polystyrene beads with two different sizes; those with 260-nm diameter entered the pores (see the figure, with empty and filled pores enlarged) while 320-nm ones did not. The measured band-edge redshifts were then used to calibrate the simulations and predict detection limits. Theoretically, as few as 10 vaccinia viruses could be detected with the PC, comparable to other biodetection methods. Advantages accrue, however, from the small sensor size, the ability to tune the geometry for different particles, and the ease of integration into lab-on-a-chip setups. The authors say that their random-binding scheme is more practical than methods that rely on binding organisms to single PC defects. (S. E. Baker et al., Appl. Phys. Lett. 97, 113701, 2010.)—Stephen G. Benka

Messenger RNA (mRNA) is the shuttle that carries genetic information across a cell’s nuclear membrane and into the cytoplasm, where the information is translated into a protein sequence. However, the movement of mRNA, which is about 25 nm in diameter, through the nuclear pore complex, roughly 120 nm in diameter, has been difficult to resolve visually since both mRNA and the NPC are well below the 200-nm diffraction limit for optical microscopes. Now, Robert Singer at Yeshiva University’s Albert Einstein College of Medicine in New York and David Grünwald at the Delft University of Technology in the Netherlands have developed a new nanometer-resolution imaging technique that they used to track mRNA’s passage. Emission signals from mRNA and the NPC—labeled with spectrally different fluorescent probes and shown in the image as green and red, respectively—were chromatically separated and tracked by two synchronized high-speed CCD cameras. The researchers achieved 26-nm spatial resolution by resolving the misalignment between the mRNA and the NPC in the images collected before and during tracking by both cameras—a technique they’ve dubbed super-registration microscopy. In their experiments, they also observed that mRNA spent about 5-20 ms crossing the NPC, a fraction of the time it spends at the pore’s entrance and exit—as if, say the researchers, the mRNA was being double screened for quality. That information may support research into understanding how defective mRNA is prevented from escaping the nucleus. (D. Grünwald, R. H. Singer, Nature, in press, doi:10.1038/nature09438.)—Jermey N. A. Matthews

Related link:

Robert Singer explains super-registration microscopy

During the collapse of a cavitation bubble, the gas inside it can reach temperatures of more than 15 000 K—as hot as the surface of a star—and the energy can be released in the form of shock waves, heat, light, turbulent vortices, and high-speed jets of fluid. For decades, medical researchers have worked to harness that energy for therapeutic applications, such as the disintegration of cancerous tumors using focused ultrasound (see the article by Gail ter Haar in Physics Today, December 2001, page 29) and the delivery of drugs or genes into living cells (see the article by Detlef Lohse in Physics Today, February 2003, page 36). Although studies have demonstrated that microbubbles can rupture nearby cells, control over the bubble–cell interaction has remained difficult. Duke University researchers led by Pei Zhong have now demonstrated an approach to puncturing a cell’s membrane that entails carefully manipulating the fluid dynamics around it. The high-speed sequence of photographs captures the process: Two laser pulses, offset in space by 40 μm and time by 4 μs, create two bubbles (B₁ and B₂) that act in concert. The rapid expansion of the second bubble causes the collapse of the first bubble by pressing against it; the interaction deforms the shape of both. The bubbles’ asymmetric collapse gives rise to two localized microjets—one toward the cell between 6 and 7 μs, one away from it 2 μs later. The researchers can control the microjets’ impact by adjusting the bubbles’ position, spacing, and orientation relative to the cell. (G. N. Sankin, F. Yuan, P. Zhong, Phys. Rev. Lett., in press.)—R. Mark Wilson

A collaboration led by Pascal Martin of the Curie Institute in Paris yoked live and virtual cells to tackle the question, How does the ear amplify faint signals by factors of up to 1000? Hearing relies on converting mechanical vibrations to electrical impulses. The transduction takes place in the cochlea and is carried out by micron-scale hairs that sprout from specialized hair cells. To the tiny hairs, the watery liquid that surrounds them is viscous, just like honey would be to a tuning fork. An active feedback mechanism in the hair cells not only overcomes the viscosity, but also amplifies faint signals. But the feedback can't provide all, or even most, of the ear's prodigious amplification. Two years ago, theorists proposed that elastic coupling among groups of hair cells could make up the shortfall. Coupling, they argued, lowers the detection threshold by averaging out each cell's noise fluctuations. Hair cells in frogs, humans, and other terrestrial vertebrates are indeed coupled to each other by various flexible structures. To prove that coupling boosts amplification, Martin's team extracted a vibration-sensing organ from a bullfrog and attached a flexible whisker to one of the hair cells (see schematic). Through sophisticated computer control, the whisker was made to vibrate in a way that mimicked the net force on the live cell (green) exerted by two neighboring hair cells (gray). The expected enhancement to the amplification showed up. (J. Barral et al., Proc. Natl. Acad. Sci. USA, in press.)—Charles Day

The outer layer of a pollen-grain wall generally includes apertures through which the grain can gain or lose water. When in an arid environment, pollen grains avoid becoming dangerously dry by undergoing a process called harmomegathy—the grain’s apertures are effectively sealed until the pollen lands in a wetter location. For more than a century, scientists have known that wall structure helps determine the form that a pollen grain assumes after harmomegathy. Now Harvard University’s Jacques Dumais, former Harvard student Eleni Katifori, and colleagues have presented the first quantitative model of the process and confirmed it with electron micrographs such as shown here (the scale bars represent 20 µm). The model incorporates the classic result that stretching a surface costs a lot of energy; instead of stretching, the grain surface bends as the wall folds onto itself to avoid further desiccation. The lily grain in panel a, for example, has an elongated aperture that allows harmomegathy to proceed somewhat like the way in which one makes a cone by connecting the edges of a disk that has had a slice removed. Strictly followed, that process yields vertices with high concentrations of bending energy; in reality the lily grain stretches a little at the vertices and ends up looking like a US football. The other grains illustrated in the figure have built on the same simple physics—avoid stretching and kinks—to achieve more intricate but equally effective harmomegathic responses. (E. Katifori et al., Proc. Natl. Acad. Sci. USA, in press, doi:10.1073/pnas.0911223107.) —Steven K. Blau

Aurélien Roux of the Curie Institute in Paris and his coworkers in Patricia Basssereau's group have cleared up one of the mysteries of how the protein dynamin helps form synaptic vesicles. Synaptic vesicles are lipid-wrapped nanoscale packets that contain neurotransmitters, the molecules that convey signals between neurons. Signaling begins when synaptic vesicles fuse with the signaling neuron's membrane, thereby releasing their contents. The neurotransmitters then diffuse across the tiny gap to the receiving neuron and bind to the neuron's surface. Once they've delivered their message, they unbind and make their way back to the signaling neuron, which retrieves them by budding fresh synaptic vesicles from its cell membrane. The protein clathrin initiates the budding by forming a curved coat on the membrane's interior surface (see figure); dynamin ties off and ultimately severs the vesicle. In solution, dynamin molecules polymerize into a spiral whose inside radius matches that of the dynamin monomers. In vivo, the spiral is seen to wrap around the necks of clathrin-coated vesicles. Roux and his team set out to determine whether the polymerization is triggered by the neck's curvature. Their experiment, which used artificial vesicles, optical tweezers, and fluorescently tagged dynamic molecules, showed that dynamin will readily polymerize around tubes whose outside radius matches dynamin's inside radius. More important, Roux and company also found that when dynamin's concentration is high enough, it will polymerize on fatter tubes and that the act of polymerizing can apply the few-piconewton force needed to squeeze a neck. (A. Roux et al., Proc. Natl. Acad. Sci. USA 107, 4141, 2010.)—Charles Day

Biological and medical researchers have long sought to study or control cellular function by inserting biomolecular probes inside the cell. But those probes, which include peptides and nucleic acids, must first cross the cell’s highly selective membrane. Traditional approaches to breaching that barrier are to chemically modify the probe or membrane and to pack the probe into a virus, which fuses to a cell’s membrane before depositing its load; both methods induce unwanted side effects and are limited to delivering specific molecular cargo. Now a team of US and South Korean scientists, led by Harvard University’s Hongkun Park, has developed a minimally invasive delivery method that exploits the ability of silicon nanowires to physically penetrate the cell’s membrane. The researchers prepared vertically aligned nanowire arrays with a density of roughly 25 million nanowires/cm² and altered their surface chemistries to enable noncovalent binding of a broad spectrum of molecules. With the nanowire platform, they were able to simultaneously assay the intracellular effects of distinct molecular probes. In one experiment, the researchers layered human fibroblasts, shown green in the scanning electron microscope image, across the nanowires, shown in blue. Nearly all of the cells were impaled within one hour and received the bound probes within 24 hours. Impaled cells continued to grow for several weeks, albeit at a slightly slower rate. (A. K. Shalek et al., Proc. Natl. Acad. Sci. USA, in press, doi:10.1073/pnas.0909350107.) — Jermey N. A. Matthews

Designers of transportation networks have to weigh the cost of serving customers against the need for an efficient, robust system. Natural organisms, too, confront tasks in which they need to balance competing desiderata. As it forages for food, for example, a slime mold must balance cost (that is, the amount of protoplasm it extrudes), efficiency, and the ability to withstand injury. Remarkably, as recently reported by Atsushi Tero and colleagues from Japan and the UK, the molds do as well as transportation engineers in balancing their analogous competing needs. Panel a of the figure re-creates a 17-cm-wide map of the principal cities served by the Tokyo railway system with a slime mold (yellow) at the location of Tokyo and food flakes (white) representing other cities. In about a day’s time, the slime mold finds where the nourishment is and generates a protoplasm network with the food flakes as nodes. Standard metrics for analyzing transportation networks reveal that the mold’s foraging network and the Tokyo railway system perform similarly. Perhaps more significantly, Tero and company imitated slime-mold networks in numerical simulations that don’t incorporate detailed biochemistry. Instead, they include a feedback step in which tubular links carrying a large protoplasm flux grow wider and flux-poor links contract. By tweaking their simulation parameters, the researchers could nudge the network toward, for example, greater cost efficiency. With optimal parameters, they could even improve upon the work of slime molds and human engineers. (A. Tero et al., Science 237, 439, 2010.) —Steven K. Blau

Unlike the branches of a tree, the network of veins in a typical leaf is full of closed loops. Even after a visit by a hungry insect, no part of the leaf is cut off from the network, as shown in the top part of the figure. But is a leaf’s fractal-like form, with loops of various sizes, the best possible network for resisting that type of damage, or might a different loop-filled structure be better? And is the hierarchical structure the optimum for any other criterion? Marcelo Magnasco (the Rockefeller University, New York) and colleagues sought to find out. Using a mathematical model that assigns each vein segment a cost proportional to its capacity raised to a power γ, they looked for the networks with a given total cost that suffered the least average strain under two sets of circumstances. First, they looked at damage to a randomly chosen vein segment. Second, they considered the case of a fluctuating load, in which the amount of fluid to be delivered to each part of the network varied in time and space. (Real leaves do sometimes need to handle fluctuating loads. So, more obviously, do most human-built networks.) They found that for low values of γ (results for γ = 0.1 are shown in the figure), both cases yielded hierarchical networks of loops, qualitatively similar to real leaves. (E. Katifori, G. J. Szöllősi, M. O. Magnasco, Phys. Rev. Lett., in press.) —Johanna Miller

Stretched out completely, a human chromosome would be several centimeters long. It is packed, along with its 45 companions, into a few-microns-wide cell nucleus in such a way that all the necessary genes are accessible to RNA transcription. Figuring out how that packing is done is no easy task. Microscopy helps, but provides nowhere near a complete picture. Now a research team led by Eric Lander of MIT and Job Dekker of the University of Massachusetts has developed a method for probing chromosomes’ folded structures. The researchers chemically join segments of a folded chromosome that are close in space, cut away and sequence the DNA around the crosslink, and compare those sequences to genome libraries to determine which parts of the chromosome are in contact. A matrix of the observed contacts, as shown in the figure, reveals large-scale organization. Analyzing the plaid pattern, the researchers found that most of the cell’s actively transcribed DNA was spatially segregated from most of the inactive DNA. On a smaller scale, chromosome segments a millimeter or so in extended length appeared to form so-called fractal globules with self-similar structures very different from that of a tangled polymer in equilibrium. So far, the researchers have studied only cultured cell lines: one derived from a tumor and another modified by a virus. They hope to apply their method to healthy cells and to look for differences in chromosome structure among cells of different types. (E. Lieberman-Aiden et al., Science 326, 289, 2009.) —Johanna Miller

Photonic devices that can detect and control the polarization of light across a range of wavelengths are rare. More common are materials such as quartz that can be made into monochromatic optical retarders, which through their intrinsic birefringence convert a specific wavelength of linearly polarized light into circularly polarized light, or vice versa. Some multilayered thin films exhibit achromatic retardation through fabricated periodic nanoscale structures that effectively combine the dispersive properties of each layer to achieve wavelength-independent birefringence. But engineering nanoscale structures is tricky, and even the best synthetic achromatic retarders perform poorly across the full visible range, varying by as much as 9.1°. But Nature has already solved the puzzle in animals that have evolved biophotonic structures for signaling, vision, and coloration (see Physics Today, January 2004, page 18). Now, an international team of researchers from the UK, Australia, and the US has discovered a near-ideal achromatic retarder in the eyes of the colorful peacock mantis shrimp, Odontodactylus scyllarus, shown in the image. This mantis shrimp’s biophotonic retarder is the R8 photoreceptor cell—a UV-photopigment-filled lipid bundle with critical radii of 26 nm and 40 nm, which are subwavelength for visible light. When subjected to linearly polarized light, the R8 cell acted as a quarter-wave retarder, converting the incident light to circularly polarized light, as confirmed by close experimental agreement with theoretically determined Stokes parameter values. Moreover, the extent of retardation varied by only 2.7° across the visible spectrum. (N. W. Roberts et al., Nat. Photonics, in press, doi:10.1038/nphoton.2009.189. Image courtesy of Roy Caldwell, University of California Berkeley.)—Jermey N. A. Matthews

In a single cell, thousands of simultaneously occurring biochemical reactions carry out such functions as converting and storing energy and regulating nutrient levels; together, those processes make up the cell’s metabolic network. Computational biology involves, among other things, the linking of metabolic pathways to form a metabolic network model, a promising tool for preclinical drug studies and other medical research. However, such computational models do not traditionally include the function-determining structural details of a network’s macromolecules; for example, an enzyme’s ability to catalyze reactions and regulate the cell’s response to external stimuli is determined by its three-dimensional configuration. Now, an international team led by Adam Godzik at the Burnham Institute for Medical Research in California has taken a rare step and introduced atomic-level protein structural data to the metabolic network model of an ancient thermophilic bacterium, Thermotoga maritima, shown in this optical microscope image. The image also shows schematics of proteins in their 3D configurations, which, when they were expressed in the reconstructed metabolic network, helped the research team solve the puzzle of how proteins evolve when their cell networks grow larger.

It turns out that only 37% of T. maritima’s proteins are essential to the formation of its metabolic network; those “core-essential” proteins adopt the bulk—61%—of the bacterium’s relatively few unique 3D configurations. The finding suggests that the core-essential proteins evolved their structure to perform additional functions in distinct pathways. (Y. Zhang et al., Science 325, 1544, 2009.)—Jermey N.A. Matthews

When a person’s head strikes, or is struck by, another object, it accelerates. As it begins to decelerate, the brain slams into the skull, then bounces off and oscillates until the impact energy dissipates. The resulting shear and compressive strains can lead to brain damage. But in battlefield explosions, just the acoustic waves alone can cause soldiers traumatic brain injuries. To better understand that process, Lawrence Livermore National Laboratory's William Moss and Michael King and the University of Rochester’s Eric Blackman compared numerical simulations of a head colliding with a wall to one being struck by an explosion’s blast waves. Despite accelerating the head at less than half the rate of the wall collision, the simulated blast produced on the brain surprisingly comparable pressure spikes—ranging up to 3 bars—and even larger pressure gradients. Apparently, those mechanical loads are delivered by the skull, which ripples under the pressure of blast waves—the rippling motion is indicated in the image by velocity vectors. The researchers confirmed the role of the skull’s elasticity by making it 1000 times stiffer in their simulations and observing a fivefold drop in the pressure spikes. The simulations also revealed that helmets in contact with the head can impart an additional mechanical load to the skull and helmets that allow for an air cushion geometrically focus and increase the magnitude of blast waves. (W. C. Moss et al., Phys. Rev. Lett., in press.)—Jermey N. A. Matthews

Dispersed in the brains of Alzheimer's patients are disk-shaped lesions, about 100 µm across. Whether those lesions, or plaques, are a cause or a consequence of Alzheimer's disease is controversial, but their composition is clear. The plaques are made from fibrous aggregates—amyloid—of protein or their shorter cousins, peptides. Once sequestered in amyloid, a protein or a peptide can no longer perform its function. Even if amyloid does not directly cause Alzheimer's and other diseases, it seems at best a useless, dead-end repository of proteinaceous material. But as a new paper exemplifies, a less malign view of amyloid is emerging. Roland Riek of ETH Zürich and his collaborators have demonstrated that our bodies exploit amyloid as a temporary storage medium for a wide range of peptide hormones. Riek suspected a hormone–amyloid connection when he found that a stress hormone formed amyloid fibrils. He and his collaborators then subjected 41 other peptide hormones to a battery of biochemical, biophysical, and crystallographic tests. The finding: 75% of the peptide hormones form amyloid; and, as befits a storage medium, the amyloid can also disaggregate to release the peptides. In a final test, the team stained slices of mouse brain with hormone-sensitive and amyloid-sensitive dyes. The stained regions coincided. Riek's discovery adds to the modest but growing list of examples of so-called functional amyloid that perform useful tasks in living organisms. Evidently, amyloid is not always pernicious. (S. K. Maji et al., Science 325, 328, 2009.)—Charles Day

The late 19th century saw a radical innovation in horse racing: Jockeys abandoned a comfortable, upright posture for the hunched-over, short-stirrup style seen today at racetracks (and in the figure). By 1910, when the style was universally adopted, race times had dropped by more than 5%; the improvement in the first decade of the 20th century was greater than in the hundred years since. One might think that the reduced aerodynamic drag of the new style led to the faster times, but Thilo Pfau and colleagues at the University of London’s Royal Veterinary College suggest that the way the modern jockey moves in response to the horse’s galloping makes the more significant contribution. The London group measured the motion of jockeys and horses and observed that jockeys do not suffer much vertical displacement as a horse races—a consequence of the way they absorb the horse’s motion by strenuously pumping their legs while riding. So, though the horse supports the jockey’s weight, it does not expend unnecessary energy lifting and lowering its cargo. Moreover, the horse’s forward speed varies over the course of a gallop cycle. When the horse is moving faster than on average, the jockey moves slower. That out-of-phase response could help the horse to execute a smoother, more energy-efficient gallop. (T. Pfau et al., Science 325, 289, 2009; photo by Pharaoh Hound) —Steven K. Blau

Lactose isn't present in our guts all the time. To ingest it and other occasional sources of nutrition, Escherichia coli (see figure) must detect the molecules and then make the proteins that help harvest them. That process of on-demand protein production is called gene regulation. It's the subject of a new quantitative analysis by physicists Ulrich Gerland of the University of Munich, Germany and Terence Hwa of the University of California, San Diego. E. coli uses two modes of gene regulation. In (+ +) control, proteins called transcription factors float freely in the cell. When a TF molecule meets its molecular target—lactose, say—it locks onto the appropriate region of the bacterium's DNA and triggers the production of the appropriate protein. In (− −) control, the TF is usually bound to the DNA and blocks protein production until TF's molecular target arrives to detach the TF and lift the block. Both modes are equally effective. When does evolution favor one over the other? The answer, according to Gerland and Hwa, depends on a tug of war between two competing selection principles. The use-it-or-lose-it principle favors (+ +) control during feasts and (− −) control during famines, whereas the wear-and-tear principle favors the opposite. Both selection principles mitigate the adverse effects of genetic mutation but, as Gerland and Hwa found, whether one prevails over the other depends on the size and age of the colony and on how rapidly the food supply fluctuates. Besides quantifying gene regulation, Gerland and Hwa's analysis might help pharmacologists understand and combat the resistance of bacteria to antibiotics. One strain of E. coli, called mar, is resistant to tetracycline, an otherwise potent antibiotic, due to the working of two transcription factors. (U. Gerland, T. Hwa, Proc. Natl. Acad. Sci. USA 106, 8841, 2009.) —Charles Day

Traveling smoothly through a turbulent medium is no mean feat, as anyone who regularly flies in an airplane can attest. Scientists have investigated how fish navigate through turbulent currents, but until recently they had not addressed the analogous issue of animal flight through turbulent air. Now biologist Stacey Combes has filmed male orchid bees (genus Euglossa) flying in turbulent airstreams and, with colleague Robert Dudley, has described the effects of the turbulent air on the bee’s flight stability and maximum speed. Combes induced the bees to fly in a turbulent airstream by luring them with an attractive scent. As the airspeed increased, the bees found it increasingly difficult to avoid the rolling illustrated in the left image. When the airspeed was high enough and maintaining stable flight difficult enough, the bees extended their hind legs, as depicted in the right photograph.

That move increased the moment of inertia about the roll axis by roughly 50% and improved stability, but it also increased body drag and energy expenditure by about 30%. In a second experiment, Combes altered the turbulence of the stream by inserting different geometric grids. Bees flying in the lower-turbulence environment were able to reach higher speeds before instabilities caused them to be ejected from the air stream. (S. A. Combes, R. Dudley, Proc. Natl. Acad. Sci. USA, doi:10.1073/pnas.0902186106.) —Steven K. Blau

Related link: Dragonfly Flight, Z. Jane Wang, Physics Today October 2008, page 74.

The unusual stiffness or sponginess of dead and decaying biological tissue is readily apparent to the human touch. However, early detection of such mechanical property changes in a tissue's extracellular matrix could signal the onset of disease. To measure the elasticity of tissue in living patients, needle-based indentation methods are more direct and less expensive alternatives to MRI, ultrasound, and electrical impedance. Such a probe has recently been developed by University of California, Santa Barbara, physicist Paul Hansma, an atomic force microscopy expert, and his collaborators. The handheld tissue diagnostic instrument (TDI) consists of a stainless steel probe, 175 µm to 1 mm in diameter depending on the tissue sample, which longitudinally oscillates at 4 Hz in a needle-thin stationary sheath. The force from the magnetically controlled oscillation of the probe produces a corresponding displacement in the tissue. The tissue's elastic modulus, or stiffness, is proportional to the slope of the force-displacement curve, and energy dissipation in the tissue is proportional to the area under that curve. The researchers measured, with millimeter spatial resolution, healthy and diseased tissue samples ranging in elastic moduli from around 1 kPa to 12 GPa. Among them were mouse breast tissue, which hardens when it becomes tumorous, and human tooth dentin (see schematic), which softens and decays when infection sets in. The researchers say the instrument could be used in the future to simultaneously test and biopsy a tumor or, if the probe is coated with antibodies, to measure single-molecule interaction forces. (P. Hansma et al., Rev. Sci. Instrum., in press.) — Jermey N. A. Matthews

The venoms from spiders, scorpions, some marine snails, and certain other animals immobilize victims by blocking ion channels that control nerve cells. The bioactive molecules in the venoms are incredibly diverse—cone snails alone produce more than 50 000 distinct peptide venoms—and researchers hope to mine them for potential pharmaceuticals that, say, kill pain or unlock diseased ion channels. Knowing the amino acid sequences would help in that effort. Typically, researchers turn to mass spectrometry, in which the peptides are fragmented and the amino acid sequence deduced, usually in combination with searching a protein database. Unfortunately, the organisms do not have sequenced genomes, so the amino acid sequence has to be determined from mass spectrometry alone. Such de novo sequencing has been hampered by an inability to produce sufficient fragmentation. Now, Beatrix Ueberheide, David Fenyö, and Brian Chait of the Rockefeller University and Paul Alewood of the University of Queensland have devised a method that solves that problem. They realized that a simple chemical trick—the conversion of cysteine, an abundant amino acid in peptide venoms, to a lysine-like charged residue—would put the molecules in a highly positively charged state. They could then be more efficiently fragmented using a technique known as electron transfer dissociation and give rise to a rich mass spectrum. As proof of principle, the team reconstructed the complete sequence for 31 distinct peptide toxins using just 7% of the venom from the gland of a single cone snail. (B. M. Ueberheide et al., Proc. Natl. Acad. Sci. USA , in press.) — R. Mark Wilson

MRI excels at revealing subtle features in soft tissue. Hydrogen nuclei are detected through the electromotive force induced in a nearby coil when their spins flip from an RF pulse. Typically, one coil transmits the pulse and another detects the induced signal. That configuration has been used in clinical settings for decades with imagers built from 1.5 T magnets. In recent years, imagers have been developed with greater field strength to boost sensitivity. But as the field increases, so does the resonance frequency required to excite nuclei. The corresponding wavelength in tissue in a 7-T magnet is about 12 cm, on par with the size of resonator coils that encircle a human head. The result: interference and standing-wave RF patterns. Those inhomogeneities in the RF field are disastrous because they perturb the image contrast between different types of tissue. A group led by Klaas Pruessmann at ETH Zürich has now solved the problem by removing the RF coils entirely and using the conductive lining in a 7-T MRI cavity as a waveguide with an antenna placed at one end. A patient inside the waveguide is exposed to a homogeneous traveling RF wave launched from the same antenna that subsequently detects the spin signals. The in vivo images of a human leg demonstrate that traveling-wave MRI (left) can excite spins more uniformly than can inductive MRI (right). The researchers speculate that, with the tight-fitting induction coils gone, patients may suffer less from claustrophobia and engineers may enjoy more design freedom. (D. O. Brunner, N. De Zanche, J. Frölich, J. Paska, K. P. Pruessmann, Nature 457, 994, 2009.) — R. Mark Wilson

To understand how babies and children learn to process music and other sounds, it's important to know what they can do at birth. Researchers in Hungary and the Netherlands, led by István Winkler of the Hungarian Academy of Science in Budapest, have found that three-day-old infants can distinguish the downbeat in a musical rhythm — that is, the "one" in "one, two, three, four." They used electroencephalography — the detecting of electrical activity in the brain via electrodes affixed to the head, as shown in the photo — to monitor the babies' reactions to a repeating synthesized drum rhythm from which notes were sporadically left out. When the omitted sound was a downbeat, the electrodes picked up a strong discriminative response, but when a note in any other position was left out, the infants' response was much weaker. In music played by human musicians, the downbeat is often longer or louder than the surrounding notes, but that was not the case for the computer-generated sound sequence used in the experiment: The downbeat was distinguished by the arrangement of sounds alone. The result suggests that beat perception is either innate or learned in the womb. (I. Winkler et al., Proc. Nat. Acad. Sci. USA, in press; photo courtesy of Gábor Stefanics, Hungarian Academy of Sciences.) — Johanna L. Miller

X-ray crystallography routinely yields the structures of proteins with 0.1-nm resolution. But how does one take a detailed look at something far bigger―a chromosome, say, or a cell nucleus? Such objects don't crystallize, because no two individual examples have the same shape. And at a micron or so in size, they're too thick for electron microscopy. X rays, of course, pass through whole animals, not just single cells. For the past decade, the practitioners of a technique called x-ray diffraction microscopy have been steadily improving their ability to image single, biological samples. XDM's latest milestone is shown here. Made at the SPring-8 synchrotron in Sayo, Japan, this image of a pair of human chromosomes is the first from XDM in three dimensions. In general, determining a structure from a diffraction pattern requires obtaining the phases of the scattered photons. Those phases are lost when the diffraction pattern of a crystalline sample is detected; ingenious methods are needed to recover them. In XDM, the phases remain within the continuous diffraction pattern cast by the isolated sample. If the pattern is measured on a fine enough spatial scale, a computer algorithm can yield the structure by iterating between real space and diffraction space. The multiple exposures required to create this three-dimensional image damaged the sample and limited resolution to 120 nm. In principle, further improvements could push the resolution down to 10 nm. (Y. Nishino et al., Phys. Rev. Lett. 102, 018101, 2009.) ― Charles Day

To map molecules in cells and tissue, researchers prefer biomedical imaging techniques that rely solely on the intrinsic responses of chemical bonds to optical stimulation. Although fluorescence microscopy and other chemical tagging methods yield high-resolution images, they also introduce foreign species or synthetic derivatives that can alter the dynamics of intracellular processes. Spontaneous Raman scattering, which uses a single laser beam to excite the vibrational and rotational modes in chemical bonds, requires no chemical labels but generates a weak signal that gets muddled by Rayleigh scattering. A more sensitive technique known as coherent anti-Stokes Raman scattering uses multiple laser beams to generate coherent optical signals that enhance resonant frequencies in the sample; that method, however, also produces nonresonant background noise. Recently a team led by Harvard University chemist Sunney Xie demonstrated a new technique based on stimulated Raman scattering that tunes the difference between the frequencies of two laser beams to match a desired molecule's resonant frequency, thus amplifying the Raman signal. The measurable intensities of the transmitted beams change only when a match occurs; nonresonant signals are not picked up. The images show the top view (a) and the depth profile (b) of an acne medication (blue) that penetrated a mouse's skin, thus demonstrating the potential of the new technique to monitor drug delivery. (C. W. Freudiger et al., Science 322, 1857, 2008.)
— Jermey N. A. Matthews

With their ability to manipulate microliter to nanoliter volumes of liquids, microfluidic devices have found increasing application in a variety of fields, from ink-jet technology to proteomics and DNA analysis. Most current microfluidic devices are made from glass or polymers, and advances in design and fabrication have opened the realm of three-dimensional, complex flow paths. George Whitesides and colleagues at Harvard University have recently demonstrated 3D devices made from stacked layers of ordinary paper and tape. Thanks to paper's wicking ability, the devices don't require external pumps to drive the liquids through. Indeed, the wicking property of paper is routinely exploited in medical tests such as those for blood glucose, pregnancy, and HIV. To define the microfluidic pathways in the paper-based microfluidic device, the team impregnated each paper layer with a common photoresist, a hydrophobic polymer that could be patterned with UV light. With their channels thus established, the layers of paper were alternated with layers of double-sided tape; holes cut in the tape connected channels in adjacent paper layers. The figure illustrates the complex routing that can be achieved: Four differently colored liquids deposited on the top of a 5 cm × 5 cm, nine-layer stack (left) are, within 5 minutes, wicked through horizontally and vertically to the array of 1024 detection zones on the bottom (right). With reagents or antibodies placed in detection zones prior to assembly, such devices would provide highly parallel, independent assays. The Harvard team sees particular potential for their paper-based devices in medical diagnostics in developing countries. (A. W. Martinez, S. T. Phillips, G. M. Whitesides, Proc. Natl. Acad. Sci. USA, in press.) — Richard J. Fitzgerald

Soft biological tissue is often subjected to forces that affect the tissue’s geometry, and finite elasticity provides a robust theoretical framework for analyzing the mechanical behavior of those tissues. Although the theory can accommodate anisotropic, nonlinear, and inhomogeneous processes subjected to large stresses and strains, its complexity makes many problems intractable. For growing tissue, though, the slow addition of cells generates shape- or size-changing stresses that are small enough to model successfully (see PHYSICS TODAY, April 2007, page 20). So, too, are simple geometries for tissues in equilibrium, even after those tissues are subjected to large stresses. Two recent papers have looked at applying the theory to those cases in thin elastic disks. In one recent study, Julien Dervaux and Martine Ben Amar (both of École Normale Supérieure, Paris) looked at anisotropic growth rates: If growth was faster in the radial than in the circumferential direction, the disk became conelike, while a reversal of rates generated saddle shapes. A separate study by Jemal Guven (National Autonomous University of Mexico) along with Martin Müller (ENS) and Ben Amar looked at excessively large circumferences for a given radius. Using the fully nonlinear theory, the researchers found an infinity of quantized equilibrium states for an ever-increasing perimeter at fixed radius. The ripples around the edge grew in size and number—not unlike the flower petals shown here—eventually crowding together enough to touch, like the ruffled collar in a portrait by Rembrandt. For more on the elasticity of thin sheets, see the article in PHYSICS TODAY, February 2007, page 33. (J. Dervaux, M. Ben Amar, Phys. Rev. Lett. 101, 068101, 2008; M. M. Mueller, M. Ben Amar, J. Guven, Phys. Rev. Lett., in press.) — Stephen G. Benka

How do genetic mutations, which occur in single molecules of DNA, lead to changes that help an organism of 10²³ or so molecules adapt to its environment? To answer that fundamental question, Shozo Yokoyama of Emory University and his colleagues looked at proteins called opsins, which help fish and other animals see in dim light. The molecule ultimately responsible for vision is retinal. Isolated retinal absorbs in the UV, but when it's swaddled by an opsin, the pigment's peak absorption shifts redward. Depending on its amino acid sequence, an opsin can shift the peak all the way to the IR. Fish exploit that tuning to evade predators during a particularly dangerous time of day, twilight. In shallow, clear water, the twilight spectrum peaks broadly between 400 nm (violet) and 500 nm (green). In deep water, the spectrum narrows around a peak at 480 nm (blue). And in shallow, muddy water, the spectrum shifts to the red. As you might expect, fish that swim in those different environments have opsins that engender an appropriate, survival-enhancing shift. To find evidence that those shifts arose through evolution, the Emory team first applied a statistical technique called phylogenetic reconstruction to the genetic sequences of 38 opsins drawn from various fish and other vertebrates. The result was an opsin family tree whose trunk springs from the first ancestral fish. Each node of the tree, downstream of the trunk and upstream of the present-day vertebrates, represents the opsin of an extinct species. The Emory team reconstructed those ancestral opsins in the lab, equipped them with retinal molecules, and measured their peak absorption. The combination of spectral measurements and genetic sequences revealed which DNA mutations―that is, amino acid substitutions―were responsible for the shift in peak wavelength. The results were surprising: Identical substitutions didn't always produce the same shift; substitutions that produce a significant shift didn't have to take place in amino acids that lie close to retinal; quite different substitutions yielded the same shift. The results show how hard it is to identify productive mutations and to predict their effect. Showing conclusively how the survival of the fittest plays out on the molecular level would require reconstructing not only the protein, but also the whole animal and its long-lost habitat. Still, the Emory researchers did find one piece of reassuring evidence: The opsin of the first fish tuned retinal to absorb at 501 nm, which is consistent with the shallow-water habitat of its fossilized remains. (S. Yokoyama et al., Proc. Natl. Acad. Sci. USA, in press.) ― Charles Day