The Microbial World
Special Online Collection

Advances in genome-sequencing technology are allowing previously uncultured organisms to be probed in their natural environments, whether they live intimately with us in our guts or in the far, deep sludge of the ocean's abyss. In the 23 May 2008 issue, Science and its online companion Science Signaling explored the stunning diversity and dynamics of the microbial universe. In Science, News stories looked at the hidden microbial world inside sponges and the challenges of developing a solid microbe classification system, while Review articles described the microbial processes that drive earth's biogeochemical cycles and approaches to understanding the distribution of microbial taxa and their traits. Elsewhere in the magazine, News stories and research papers investigated topics from the resident microbes on human skin and in mammalian guts to life beneath the ocean floor, and an Editorial discussed using microbes to help address society's energy, environmental, and food challenges. In Science Signaling, three Perspectives explored how different plant pathogens use similar signaling molecules in distinct ways, how gut microbes dampen the host immune response, and how mast cells use extracellular traps to kill microbes.


Airborne Pollutants and Inflammation

Inhalation of particulate airborne pollutants, such as asbestos and silica, can cause inflammation of the lungs, fibrosis, and lung cancer. How these substances exert their effects, however, is poorly understood. In a Report in the 2 May 2008 Science, Dostert et al. (published online 10 Apr) provided important molecular insights into how noxious inhaled particles lead to inflammation and disease. The team showed that asbestos and silica are sensed by a multiprotein complex known as the Nalp3 inflammasome, whose subsequent activation leads to a potent inflammatory response. Activation of the inflammasome is triggered by reactive oxygen species, which are released by immune cells (macrophages) in an effort to neutralize engulfed pathogens or toxins. The team also found that mice deficient in Nalp3 showed reduced lung inflammation in response to asbestos inhalation, supporting the idea that this inflammatory sensing complex plays a key role in the response to respiratory pollutants. The researchers further suggest than Anakinra, a drug used in the treatment of autoinflammatory syndromes including rheumatoid arthritis, might be used to slow down the progression of asbestosis, silicosis, and possible other inflammatory lung diseases. An accompanying Perspective by L.A.J. O'Neill highlighted the study.


Water-Assisted Feeding

Water molecules are attracted more to each other than they are to air. The resulting surface tension makes it possible for water to flow to the tops of trees (capillary action) and allows some insects to walk on water. In a Report in the 16 May 2008 Science, Prakash et al. demonstrated the importance of this surface tension to the feeding mechanism of long-beaked shorebirds called phalaropes. By swimming in a tight circle on the water surface, the bird first generates a vortex that draws underlying fluid and suspended prey (crustaceans or other invertebrates) toward the surface. As it spins, it dips its beaks into the water, capturing a drop of fluid and food between the halves of the beak. The geometry of the bird's open beak prevents suction from being used to raise the drops mouthward. Instead, by repeatedly opening and closing its beak in a tweezering motion, the bird moves the drop from the tip of its beak to its mouth in a stepwise ratcheting fashion. In laboratory experiments with a mechanical beak, the researchers showed that the beak geometry and wetting properties, as well as the dynamics of tweezering, can be tuned to optimize transport efficiency. Senior author Dr. John Bush talked about the work in a related podcast interview, and a related Perspective by M.W. Denny discussed how "[c]ollaboration among biologists, engineers, mathematicians, and physicists has produced exciting advances in our understanding of surface tension's effects in both nature and technology."


Circadian Insights

Circadian rhythms are daily rhythmic variations in physiology and behavior that are found in organisms as diverse as animals, plants, and fungi. Two Reports in Science this month offered new insights into circadian timekeeping in mammals.

--O'Neill et al. (16 May 2008) identified adenosine 3',5'-monophosphate (cAMP) signaling in the mouse suprachiasmatic nuclei (located in the hypothalamus) as a core component of the mammalian circadian pacemaker. The team showed that rhythmic oscillations in cAMP-mediated cytoplasmic signaling sustain transcriptional feedback loops -- whereby circadian genes are periodically suppressed by their protein products -- and determine the fundamental pacemaker properties of amplitude, phase, and period. An accompanying Perspective by M.C. Harrisingh and M.N. Nitabach discussed how models of circadian timekeeping mechanisms in plants and flies, as well as mammals, are expanding to include intracellular small-molecule signals.

--Fuller et al. (23 May 2008) found that in addition to the light-driven circadian clock that resides in the suprachiasmatic nucleus, the mouse brain (and presumably the brains of other mammals) contains a second circadian clock -- located in the dorsomedial hypothalamus -- that is entrained by food. Their data indicate that this second clock can override the light-entrained clock when the animal is faced with limited food, thus taking over control of functions such as wake/sleep rhythms and activity levels so they can match the availability of food. Senior author Dr. Cliff Saper discussed the work in a related podcast interview.


Self-Organizing Division Machinery

One way to understand a complex biological process is to reconstitute it from purified components in vitro. Two Reports in the 9 May 2008 Science demonstrated that even the intricacies of cell division can be reconstituted in a cell-free system. In bacteria, so-called Min proteins oscillate from end to end of a cell to select the appropriate division site. Loose et al. found that in a simple in vitro system containing a lipid bilayer to mimic the cell membrane and ATP for energy, two Min proteins -- MinD and MinE -- self-organize into waves and spirals along the bilayer. These dynamic patterns persisted for hours and could account for the behavior of these proteins in vivo. In another study, Osawa et al. (published online 17 Apr) focused on FtsZ, a tubulin homolog, and the primary cell division proteins in most bacteria and archaea. It is tethered to the membrane by FtsA, and together with a dozen other proteins, assembles into the Z ring which constricts to divide the cell. The team constructed a membrane-tethered FtsZ (eliminating the need for FtsA) and showed that that when mixed with simple lipid vesicles, FtsZ spontaneously assembled into multiple Z rings that formed indentations along the vesicles. These findings suggest that FtsZ itself can assemble the Z ring and generate the force capable of initiating constriction of a dividing cell. An accompanying Perspective by J. Lutkenhaus highlighted the studies.


Nouns in the Brain

The question of how the human brain represents and organizes conceptual knowledge seems impossibly complicated to answer, given how even simple nouns, such as "celery," might be expected to activate neurons in various areas, such as those involved in eating and tasting. In a Research Article in the 30 May 2008 Science, Mitchell et al. described a computational model that can actually predict the human brain activity associated with the meanings of nouns. The model is based upon a theory that represents nouns as 25-dimensional vectors, where each dimension is a sensory-motor feature such as eating or smelling. The vectors are computed from the co-occurrences of words within a trillion-word text catalog that captures typical word use. The researchers "trained" the model with observed functional magnetic resonance imaging (fMRI) data from subjects presented with 60 images of concrete nouns (such as "celery," "foot," and "cow") and found that it can identify a noun that has not been included in the training set and predict the pattern of neural activity when a subject is shown a picture of a new noun. The results thus establish a direct, predictive relationship between the statistics of word co-occurrence in text and the neural activation associated with thinking about word meanings.


Seaweed and the First Americans

Monte Verde, Chile provides some of the best evidence for the early peopling of the Americas prior to the widespread Paleo-Indian Clovis culture. In a Report in the 9 May 2008 Science, Dillehay et al. presented carbon-14 dates of seaweed discovered at Monte Verde that further reinforce the site's antiquity and provide evidence that its early settlers used a variety of marine resources. While sifting through previously excavated sediments from hearths and braziers, the team recovered the remains of nine species of marine algae as well as three stone tools -- one with seaweed remains on its working edge. Accelerator mass spectrometry on two samples dates them to about 14,000 years ago, which is consistent with dates derived from wood artifacts and charcoal found at the site. Many of the species are edible and are used today as medicinal plants by local indigenous people. Moreover, the species represent different environments (marine, estuarine, and terrestrial coastline), and differences in seasonal availability, both of which suggest that early Monte Verdeans had an intimate familiarity with these coastal resources. The data also lend support to the idea that early settlement of South America took place along the Pacific coast. A News story by M. Balter highlighted the Report.


Probing Martian Land and Ice

Two studies in Science this month presented analyses of martian mineral and ice deposits -- made possible by instruments aboard the Spirit rover and Mars Reconnaissance Orbiter -- that offer new insights into the geologic history and ancient environmental conditions on the red planet.

--Squyers et al. (23 May 2008) reported the discovery of silica-rich deposits on Mars by the rover Spirit. Thermal emission data show that the deposits -- which include nodules on an outcrop, rock samples, and light-colored soil turned up by the rover wheels -- are opaline silica (as opposed to crystalline forms like quartz) and are likely to have formed by hydrothermal activity at low pH, perhaps associated with volcanism. As noted by Dr. Squyres in a related podcast interview, the discovery is particularly important for understanding the past habitability of Mars because hydrothermal environments on Earth support thriving microbial ecosystems.

--Phillips et al. (30 May 2008, published online 15 May) presented radar sounding data, captured by the Mars Reconnaissance Orbiter, of the planet's thick north polar ice cap. The data reveal four dust-rich layers, separated by layers of nearly pure ice, that can be explained by likely variations in Mars' orbit or axial tilt (see the News story by R.A Kerr in the 16 May issue). The polar cap only slightly depresses the underlying crust, which implies that the lithosphere beneath the cap is more than 300 km thick. And because the stiffness of the rocks is connected to temperature, the findings also imply that the martian interior is extremely cold. An accompanying Perspective by M. Grott discussed how the new data challenge current notions about the planet's geologic and thermal history.


Echoes of a Supernova Explosion

Cassiopeia A is the youngest supernova remnant known in the Milky Way galaxy and the brightest radio emitter in the sky. Based on its observed expansion, astronomers estimate that the explosion that produced it occurred about 300 years ago. Due to the lack of recorded observations at the time of the explosion, however, little is known about what kind of supernova it originated from. Now, in a study in the 30 May 2008 Science, Krause et al. report observations of a scattered "light echo" of Cassiopeia A, three centuries after the direct light from the explosion swept past Earth. Taken with a multiband imaging photometer instrument aboard the Spitzer Space Telescope, the spectrum shows that Cassiopeia A was a type IIb supernova and originated from the collapse of the helium core of a red supergiant star that had lost most of its hydrogen envelope before exploding. An accompanying Perspective by A.C. Fabian and a podcast interview with lead author of the study, Dr. Oliver Krause, highlighted the findings.


Ocean Oxygen Loss

Because the solubility of oxygen decreases as water temperature increases, climate models predict an overall decline in oceanic dissolved oxygen concentration as a result of global warming. This could have dramatic consequences for marine life and coastal economies. In a Report in the 2 May 2008 Science, Stramma et al. constructed 50-year time series of dissolved oxygen concentrations in the tropical Atlantic and equatorial Pacific using historic data and recently measured oxygen profiles. Consistent with model predictions, levels of dissolved oxygen have dropped in some cases by more than 15% during the past 5 decades. Moreover, the time series show a clear vertical expansion of low-oxygen zones, particularly in the eastern tropical Atlantic. Given that these trends affect carbon and nitrogen cycles, and have important implications for marine ecoystems and fisheries resource management issues, continued global ocean measurements of dissolved oxygen concentrations are needed. A ScienceNOW story by P. Berardelli highlighted the study.


How the Sahara Dried

One of the most dramatic environmental changes of the past 10,000 years has been the transition of northern Africa from a "green Sahara" to the world's largest desert. Desiccation has eradicated all but a few natural archives recording this transition, thus hampering efforts to discern exactly when and how fast the Sahara dried out. In a Research Article in the 9 May 2008 Science, Kröpelin et al. reported on a lake sediment record that sheds new light on the history of Saharan climate and ecosystem change (see the related ScienceNOW story by M. Tatalovic). The record comes from Lake Yao in northern Chad, one of the few Saharan lakes in which sediments have continuously accumulated during the past 11,500 years. Analysis of salinity and dust deposition, as well as biological indicators such as pollen, spores, and the remains of aquatic biota, reveal a gradual change in the ecosystem that took place from 6000 to 2700 years ago -- not an abrupt change as has been hypothesized. The data show a slow reduction in the abundance of tropical vegetation, followed by the loss of grass cover, and the eventual establishment of the desert plant community of today. Dr. Kröpelin discussed the work in a related podcast interview, and an accompanying Perspective by J.A. Holmes highlighted the findings.


Making Stronger Steel

Stronger, tougher steels are constantly needed to improve safety in transportation, architectural flexibility in construction, and performance in heavy machinery. For structural steels to maintain their strength and toughness, however, they cannot be used at temperatures below the so called ductile-brittle transition temperature -- at which the metal starts to weaken and fracture. Avoiding this problem usually requires the addition of a number of alloying elements that can substantially raise the cost of the steel. Now, in a study in the 23 May 2008 Science, Kimura et al. report on the development of low-alloy steel that grows stronger and tougher as the temperature is lowered. The team processed the steel through a combination of grain refinement and precipitation hardening to produce an elongated grain structure and fibrous texture that resists cracking. This approach does not require adding a large amount of alloy elements and surpasses the toughness of maraging steel, which is the strongest structural material used today. An accompanying Perspective by J. W. Morris Jr. noted that "[a]s advances in the understanding of brittle fracture and the control of microstructure feed into the design of new structural steels, more exciting results of this kind can be expected."


Unified Laser Theory

From CD and DVD players to fiber optic communications, laser technology has become a common presence in everyday life. The design of most laser devices relies on our understanding of conventional lasers, in which light is tightly confined between two mirrors that define a resonant cavity, leading to the build-up of a coherent excited state and subsequent emission into a single optical mode. However, advances in nanofabrication techniques have led to the development of novel laser systems whose description falls outside the scope of conventional laser theory. In so-called diffuse random lasers, for example, a set of particles embedded in an active material scatter light without a light-confinement mechanism. In a Report in the 2 May 2008 Science, Türeci et al. described a theoretical approach to understanding the nature of lasing in these complex structures. The researchers explain that there is competition between different excitation modes and that the interaction of these modes ultimately determines both the emitted frequencies of the random lasers and their corresponding intensities. As noted in an accompanying Perspective by J. Bravo-Abad and M. Soljacic, the new theory "may inspire the design of substantially different classes of structures that could be the basis of improved laser-based devices."



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In Science Signaling

VGF and Antidepressant Responses

Recent studies have identified adaptations of intracellular signaling pathways and target genes that could contribute or modulate the action of antidepressant drugs, as well as exercise-mediated antidepressant responses. There is also growing evidence that growth factors may be important mediators of antidepressant responses. In a Perspective in the 6 May 2008 issue, J.E. Malberg and L.M. Monteggia highlighted two independent studies whose results suggest that VGF, a neuropeptide previously shown to be involved in maintaining organismal energy balance and mediating hippocampal synaptic plasticity, may also be involved in mediating antidepressant responses. Whereas one group sought to identify downstream targets of exercise, and the other focused on gene expression changes that were common following elevation of two putative mediators of antidepressant efficacy, both groups identified VGF. This suggests a point of convergence between exercise and antidepressant signaling. The groups also examined the behavioral effect of VGF in rodent models of depression and found that VGF infusions into the brain altered the behavior of the animals similar to effects observed following exercise or administration of antidepressants. Further studies will be needed to elucidate the mechanism(s) by which VGF exerts its effects.

Also in Science Signaling this month:
--E.M. Adler and A.M VanHook, in a podcast, explained how some glial cells can generate action potentials and are hypersensitive to ischemic injury (6 May 2008)
--W.G. Cance and V.M. Golubovskaya discussed how interactions between focal adhesion kinase and the tumor suppressor protein p53 affect cell survival (20 May 2008)
--A.R. Kay and K. Toth reviewed the evidence for zinc as a regulator of synaptic activity (13 May 2008)
--A new section featuring online information about experimental design, methods, reagents, and data analysis was added to ST NetWatch