Design principles of a bacterial signalling network

Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology. We experimentally determine the extent of intercellular variations in the expression levels of chemotaxis proteins and use computer simulations to quantify the robustness of several hypothetical chemotaxis pathway topologies to such gene expression noise. We demonstrate that among these topologies the experimentally established chemotaxis network of Escherichia coli has the smallest sufficiently robust network structure, allowing accurate chemotactic response for almost all individuals within a population. Our results suggest that this pathway has evolved to show an optimal chemotactic performance while minimizing the cost of resources associated with high levels of protein expression. Moreover, the underlying topological design principles compensating for intercellular variations seem to be highly conserved among bacterial chemosensory systems.     

The optical afterglow of the short gamma-ray burst GRB 050709

It has long been known that there are two classes of gamma-ray bursts (GRBs), mainly distinguished by their durations. The breakthrough in our understanding of long-duration GRBs (those lasting more than approximately 2 s), which ultimately linked them with energetic type Ic supernovae, came from the discovery of their long-lived X-ray and optical 'afterglows', when precise and rapid localizations of the sources could finally be obtained. X-ray localizations have recently become available for short (duration <2 s) GRBs, which have evaded optical detection for more than 30 years. Here we report the first discovery of transient optical emission (R-band magnitude approximately 23) associated with a short burst: GRB 050709. The optical afterglow was localized with subarcsecond accuracy, and lies in the outskirts of a blue dwarf galaxy. The optical and X-ray afterglow properties 34 h after the GRB are reminiscent of the afterglows of long GRBs, which are attributable to synchrotron emission from ultrarelativistic ejecta. We did not, however, detect a supernova, as found in most nearby long GRB afterglows, which suggests a different origin for the short GRBs.     

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.     

Geophysics: hot fluids or rock in eclogite metamorphism?

The mechanisms by which mafic rocks become converted to denser eclogite in the lower crust and mantle are fundamental to our understanding of subduction, mountain building and the long-term geochemical evolution of Earth. Based on larger-than-expected gradients in argon isotopes, Camacho et al. propose a new explanation--co-seismic injection of hot (700 degrees C) aqueous fluids into much colder (400 degrees C) crust--for the localized nature of eclogite metamorphism during Caledonian crustal thickening, as recorded in the rocks of Holsn?y in the Bergen arcs, western Norway. We have studied these unusual rocks, which were thoroughly dehydrated under granulite facies conditions during a Neoproterozoic event (about 945 million years (945 Myr) ago); we also concluded that fracture-hosted fluids were essential as catalysts and components in the conversion to eclogite about 425 Myr ago. However, we are sceptical of the assertion by Camacho et al. that eclogite temperatures were reached only in the vicinity of fluid-filled fractures. Determining whether these rocks were strong enough to fracture at depths of 50 km because they were cold or because they were very dry is crucial to understanding the mechanics of the lower crust in mountain belts, including, for example, the causes of seismicity in the Indian plate beneath the modern Himalayas.     

Reframing Architecture

I would like to thank Prof. Stephen Read (2011) and Prof. Andrew Benjamin (2011) for both giving inspiring and elaborate comments on my article “Dwelling in-between walls: the architectural surround”. As I will try to demonstrate below, their two different responses not only supplement my article very nicely, but also augment each other’s. In the beginning of Read’s comment, as he sets the stage for his observations, he unknowingly also points in the direction of Benjamin’s remarks: “I propose not to de-construct therefore, or add a point of view from an orthogonal position, but to try in the spirit of multidisciplinarity to talk in languages not well practiced—to begin to build what Bowker and Star call ‘boundary objects’ between different starting positions; points we can gather around to think further together” (Read 2011). Whereas Read facilitates a multidisciplinary dialogue, Benjamin focuses on how the absence of an initial distinction might threaten the endeavour of my paper. In my reply to Read and Benjamin, I will discuss their suggestions and arguments, while at the same time hopefully clarifying the postphenomenological approach to architecture.