Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.     

Nonlinear material behaviour of spider silk yields robust webs

Natural materials are renowned for exquisite designs that optimize function, as illustrated by the elasticity of blood vessels, the toughness of bone and the protection offered by nacre. Particularly intriguing are spider silks, with studies having explored properties ranging from their protein sequence to the geometry of a web. This material system, highly adapted to meet a spider's many needs, has superior mechanical properties. In spite of much research into the molecular design underpinning the outstanding performance of silk fibres, and into the mechanical characteristics of web-like structures, it remains unknown how the mechanical characteristics of spider silk contribute to the integrity and performance of a spider web. Here we report web deformation experiments and simulations that identify the nonlinear response of silk threads to stress--involving softening at a yield point and substantial stiffening at large strain until failure--as being crucial to localize load-induced deformation and resulting in mechanically robust spider webs. Control simulations confirmed that a nonlinear stress response results in superior resistance to structural defects in the web compared to linear elastic or elastic-plastic (softening) material behaviour. We also show that under distributed loads, such as those exerted by wind, the stiff behaviour of silk under small deformation, before the yield point, is essential in maintaining the web's structural integrity. The superior performance of silk in webs is therefore not due merely to its exceptional ultimate strength and strain, but arises from the nonlinear response of silk threads to strain and their geometrical arrangement in a web.     

Testing agile requirements models

This paper discusses a model-based approach to validate software requirements in agile development processes by simulation and in particular automated testing. The use of models as central development artifact needs to be added to the portfolio of software engineering techniques, to further increase efficiency and flexibility of the development beginning already early in the requirements definition phase. Testing requirements are some of the most important techniques to give feedback and to increase the quality of the result. Therefore testing of artifacts should be introduced as early as possible, even in the requirements definition phase.     

Low-voltage organic transistors with an amorphous molecular gate dielectric

Organic thin film transistors (TFTs) are of interest for a variety of large-area electronic applications, such as displays, sensors and electronic barcodes. One of the key problems with existing organic TFTs is their large operating voltage, which often exceeds 20 V. This is due to poor capacitive coupling through relatively thick gate dielectric layers: these dielectrics are usually either inorganic oxides or nitrides, or insulating polymers, and are often thicker than 100 nm to minimize gate leakage currents. Here we demonstrate a manufacturing process for TFTs with a 2.5-nm-thick molecular self-assembled monolayer (SAM) gate dielectric and a high-mobility organic semiconductor (pentacene). These TFTs operate with supply voltages of less than 2 V, yet have gate currents that are lower than those of advanced silicon field-effect transistors with SiO2 dielectrics. These results should therefore increase the prospects of using organic TFTs in low-power applications (such as portable devices). Moreover, molecular SAMs may even be of interest for advanced silicon transistors where the continued reduction in dielectric thickness leads to ever greater gate leakage and power dissipation.     

Dynamic predictive coding by the retina

Retinal ganglion cells convey the visual image from the eye to the brain. They generally encode local differences in space and changes in time rather than the raw image intensity. This can be seen as a strategy of predictive coding, adapted through evolution to the average image statistics of the natural environment. Yet animals encounter many environments with visual statistics different from the average scene. Here we show that when this happens, the retina adjusts its processing dynamically. The spatio-temporal receptive fields of retinal ganglion cells change after a few seconds in a new environment. The changes are adaptive, in that the new receptive field improves predictive coding under the new image statistics. We show that a network model with plastic synapses can account for the large variety of observed adaptations.