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New and Exciting in PLoS this week

There are many new articles in four PLoS journals today. As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers. You can now also easily place articles on various social services (CiteULike, Mendeley, Connotea, Stumbleupon, Facebook and Digg) with just one click. Here are my own picks for the week – you go and look for your own favourites:

Barcoding Life to Conserve Biological Diversity: Beyond the Taxonomic Imperative:

In the 250 years since the Swedish scientist Carl Linnaeus first started classifying organisms, taxonomists have formally described roughly 1.7 million species. Although seemingly large, this number represents only a small fraction of the estimated tens of millions of species on the planet. Moreover, human activities are causing the extinction of species hundreds of times faster than the natural rate of extinction found in the fossil record. Fully one-third of all species on the planet may be gone by the end of this century–many without ever having been studied or, more importantly, protected [1].

DNA barcoding, developed in 2003 to identify species, has helped to rejuvenate taxonomic research. The science of taxonomy is key to understanding and monitoring biodiversity [2]. The technique is based on a simple but powerful observation: that sequence diversity, in short, standardized gene regions (i.e., DNA barcodes), can serve as a tool to identify known species and potentially discover new ones. Moreover, DNA barcoding allows researchers to develop a system for species identification based on digital characters, eventually allowing for automated identifications, thereby promising to improve the capacity to identify, monitor, and manage biodiversity, with profound societal and economic benefits. It also raises the possibility of identifying the vectors of zoonotic diseases as well as the disease organisms themselves.

Left to Their Own Devices: Breakdowns in United States Medical Device Premarket Review:

Medical devices encompass nearly every medical product that does not achieve its intended purpose through chemical action, from the simple (tongue blades) to the complex (MRI machines), and from the safe (stethoscopes) to the risky (artificial hearts) [1],[2]. Certain drug-device combinations, such as drug-eluting coronary stents, are also regulated as devices.

The number and complexity of medical devices have increased dramatically over the past several decades, often to the betterment of patients’ health. Between 1997 and 2006, the value of device sales roughly doubled to US$123 billion, representing a fairly consistent 6% of the nation’s health care expenditures [3].

The Center for Devices and Radiological Health (CDRH) at the Food and Drug Administration (FDA) is charged with ensuring the safety and effectiveness of medical devices. While a number of serious safety problems with devices have emerged–the Dalkon Shield [4], the Bjork-Shiley heart valve [5], and the Sprint Fidelis defibrillator lead [6], to name a few–problems with effectiveness are not as readily apparent once a device is on the market, in part because postmarket efficacy trials of approved devices are rare. Thus, the burden of ensuring device effectiveness is heavily weighted toward premarket evaluation.

Phylogenetic and Morphologic Analyses of a Coastal Fish Reveals a Marine Biogeographic Break of Terrestrial Origin in the Southern Caribbean:

Marine allopatric speciation involves interplay between intrinsic organismal properties and extrinsic factors. However, the relative contribution of each depends on the taxon under study and its geographic context. Utilizing sea catfishes in the Cathorops mapale species group, this study tests the hypothesis that both reproductive strategies conferring limited dispersal opportunities and an apparent geomorphologic barrier in the Southern Caribbean have promoted speciation in this group from a little studied area of the world. Mitochondrial gene sequences were obtained from representatives of the Cathorops mapale species group across its distributional range from Colombia to Venezuela. Morphometric and meristic analyses were also done to assess morphologic variation. Along a ~2000 km transect, two major lineages, Cathorops sp. and C. mapale, were identified by levels of genetic differentiation, phylogenetic reconstructions, and morphological analyses. The lineages are separated by ~150 km at the Santa Marta Massif (SMM) in Colombia. The northward displacement of the SMM into the Caribbean in the early Pleistocene altered the geomorphology of the continental margin, ultimately disrupting the natural habitat of C. mapale. The estimated ~0.86 my divergence of the lineages from a common ancestor coincides with the timing of the SMM displacement at ~0.78 my. Results presented here support the hypothesis that organismal properties as well as extrinsic factors lead to diversification of the Cathorops mapale group along the northern coast of South America. While a lack of pelagic larval stages and ecological specialization are forces impacting this process, the identification of the SMM as contributing to allopatric speciation in marine organisms adds to the list of recognized barriers in the Caribbean. Comparative examination of additional Southern Caribbean taxa, particularly those with varying life history traits and dispersal capabilities, will determine the extent by which the SMM has influenced marine phylogeography in the region.

Efficient Mitigation Strategies for Epidemics in Rural Regions:

Containing an epidemic at its origin is the most desirable mitigation. Epidemics have often originated in rural areas, with rural communities among the first affected. Disease dynamics in rural regions have received limited attention, and results of general studies cannot be directly applied since population densities and human mobility factors are very different in rural regions from those in cities. We create a network model of a rural community in Kansas, USA, by collecting data on the contact patterns and computing rates of contact among a sampled population. We model the impact of different mitigation strategies detecting closely connected groups of people and frequently visited locations. Within those groups and locations, we compare the effectiveness of random and targeted vaccinations using a Susceptible-Exposed-Infected-Recovered compartmental model on the contact network. Our simulations show that the targeted vaccinations of only 10% of the sampled population reduced the size of the epidemic by 34.5%. Additionally, if 10% of the population visiting one of the most popular locations is randomly vaccinated, the epidemic size is reduced by 19%. Our results suggest a new implementation of a highly effective strategy for targeted vaccinations through the use of popular locations in rural communities.

The Enigma of Soil Animal Species Diversity Revisited: The Role of Small-Scale Heterogeneity:

“The enigma of soil animal species diversity” was the title of a popular article by J. M. Anderson published in 1975. In that paper, Anderson provided insights on the great richness of species found in soils, but emphasized that the mechanisms contributing to the high species richness belowground were largely unknown. Yet, exploration of the mechanisms driving species richness has focused, almost exclusively, on above-ground plant and animal communities, and nearly 35 years later we have several new hypotheses but are not much closer to revealing why soils are so rich in species. One persistent but untested hypothesis is that species richness is promoted by small-scale environmental heterogeneity. To test this hypothesis we manipulated small-scale heterogeneity in soil properties in a one-year field experiment and investigated the impacts on the richness of soil fauna and evenness of the microbial communities. We found that heterogeneity substantially increased the species richness of oribatid mites, collembolans and nematodes, whereas heterogeneity had no direct influence on the evenness of either the fungal, bacterial or archaeal communities or on species richness of the large and mobile mesostigmatid mites. These results suggest that the heterogeneity-species richness relationship is scale dependent. Our results provide direct evidence for the hypothesis that small-scale heterogeneity in soils increase species richness of intermediate-sized soil fauna. The concordance of mechanisms between above and belowground communities suggests that the relationship between environmental heterogeneity and species richness may be a general property of ecological communities.

How Normal Cells Can Win the Battle for Survival Against Cancer Cells:

During the early stages of tumorigenesis, cancerous cells undergo rapid and uncontrolled cell division as they invade the surrounding tissue. How tumors create space around them to accomplish this invasion is not well understood. A recent study showed that cancerous cells in fruit flies manage this feat by inducing neighboring cells to spontaneously destroy themselves and then filling the vacated space left behind in a process known as cell competition. In this issue of PLoS Biology, Yoichiro Tamori et al. provide evidence that this battle also occurs in mammalian tissues and uncover what determines the winners and losers when cells compete.

Limbs Made to Measure:

This year marks the 150th anniversary of the birth of D’Arcy Thompson, the British biologist, classicist, and all round polymath (For more information on D’Arcy Thompson see www.darcythompson.org). Like many, he was fascinated by the appearance and structure of living matter, and in his influential book, On Growth and Form [1], he set out to describe and explain the principles of morphogenesis–the way living things grow and acquire their forms. Using a vast range of examples, from the honeycomb in beehives to the spirals in a snail’s shell, he emphasized that form should be studied in the context of growth and that to explain shape it was essential to understand the underlying mechanisms. This led to the central thesis of the book: biological forms are the result of mechanical and physical processes that should be described with mathematical precision.