The ability to quickly and reliably engineer many-component systems from libraries of standard interchangeable parts is one hallmark of modern technologies. Whether the apparent complexity of living systems will permit biological engineers to develop similar capabilities is a pressing research question. We propose to adapt existing frameworks for describing engineered devices to biological objects in order to (i) direct the refinement and use of biological 'parts' and 'devices', (ii) support research on enabling reliable composition of standard biological parts and (iii) facilitate the development of abstraction hierarchies that simplify biological engineering. We use the resulting framework to describe one engineered biological device, a genetically encoded cell-cell communication receiver named BBa_F2620. The description of the receiver is summarized via a 'datasheet' similar to those widely used in engineering. The process of refinement and characterization leading to the BBa_F2620 datasheet may serve as a starting template for producing many standardized genetically encoded objects.

When light illuminates a rough metallic surface, hotspots can appear, where the light is concentrated on the nanometre scale, producing an intense electromagnetic field. This phenomenon, called the surface enhancement effect, has a broad range of potential applications, such as the detection of weak chemical signals. Hotspots are believed to be associated with localized electromagnetic modes, caused by the randomness of the surface texture. Probing the electromagnetic field of the hotspots would offer much insight towards uncovering the mechanism generating the enhancement; however, it requires a spatial resolution of 1-2 nm, which has been a long-standing challenge in optics. The resolution of an optical microscope is limited to about half the wavelength of the incident light, approximately 200-300 nm. Although current state-of-the-art techniques, including near-field scanning optical microscopy, electron energy-loss spectroscopy, cathode luminescence imaging and two-photon photoemission imaging have subwavelength resolution, they either introduce a non-negligible amount of perturbation, complicating interpretation of the data, or operate only in a vacuum. As a result, after more than 30 years since the discovery of the surface enhancement effect, how the local field is distributed remains unknown. Here we present a technique that uses Brownian motion of single molecules to probe the local field. It enables two-dimensional imaging of the fluorescence enhancement profile of single hotspots on the surfaces of aluminium thin films and silver nanoparticle clusters, with accuracy down to 1.2 nm. Strong fluorescence enhancements, up to 54 and 136 times respectively, are observed in those two systems. This strong enhancement indicates that the local field, which decays exponentially from the peak of a hotspot, dominates the fluorescence enhancement profile.

Each step of the kinesin motor involves a force-generating molecular rearrangement. Although significant progress has been made in elucidating the broad features of the kinesin mechanochemical cycle, molecular details of the force generation mechanism remain a mystery. Recent molecular dynamics simulations have suggested a mechanism in which the forward drive is produced when the N-terminal cover strand forms a ␤-sheet with the neck linker to yield the cover-neck bundle. We tested this proposal by comparing optical trapping motility measurements of cover strand mutants with the wild-type. Motility data, as well as kinetic analyses, revealed impairment of the force-generating capacity accompanied by a greater load dependence in the mechanochemical cycle. In particular, a mutant with the cover strand deleted functioned only marginally, despite the fact that the cover strand, the Nterminal ''dangling end,'' unlike the neck linker and nucleotidebinding pocket, is not involved with any previously considered energy transduction pathway. Furthermore, a constant assisting load, likely in lieu of a power stroke, was shown to rescue forward motility in the cover strand deletion mutant. Our results support a stepping mechanism driven by dynamic cover-neck bundle formation. They also suggest a strategy to generate motors with altered mechanical characteristics by targeting the force-generating element.biological motor ͉ force generation ͉ optical trap ͉ power stroke ͉ motor protein T ranslocating motors, such as kinesins and certain myosins, form a distinct class of proteins that ''walk'' along biofilament tracks to perform a wide range of vital cellular processes (1). A fundamental, yet poorly understood aspect of these motors is the energy transduction mechanism that converts the chemical energy of ATP binding, hydrolysis, and product release into mechanical work. Kinesins and myosins appear to have a common nucleotide sensor (2, 3) yet have evolved different energy conversion mechanisms to achieve a variety of motile properties. In myosin, a series of structural changes leading to the rotation of its lever arm have been identified (4), but the details of the force generation have yet to be established.Likewise, the force generation mechanism of kinesin (herein, we mainly consider Kinesin-1) is not known. Until recently, the only mechanical element considered was the neck linker (NL), which connects the N-terminal motor head to the ␣-helical stalk. This Ϸ12-residue segment is disordered and flexible in the absence of ATP and ''docks'' when ATP binds to the motor head (5). Mutations in the NL impair the motility while preserving ATPase activity and microtubule (MT) binding (6, 7). However, a mechanism for its contribution to force generation is not available, and, in lieu of this, affinity-driven zippering of the NL to the motor head has been assumed. Unlike the structurally well-defined lever arm of myosin, the NL is short and flexible when detached. Furthermore, it interacts only weakly with the motor head (8), drawing f...

[1] We report on measurements of ionospheric plasma dynamics conducted at the Arecibo Observatory between 20:00 and 24:00 local time (LT) on December 25 and 26, 2004 using the 430 MHz incoherent scatter radar (ISR). For interpretive purposes these measurements are supported by data from two nearby ionosondes and Global Positioning System (GPS) satellites. The ISR detected different ionospheric behaviors during the vertical-transmission periods on the consecutive, magnetically quiet nights. On the night of December 25 the ionosphere descended smoothly and spread F signatures faded. For about two hours on the following evening the bottomside ionosphere rose by $50 km, inducing plasma irregularities and intense spread F. Alternating cycles of bottom-side plasma rising and falling persisted through the remainder of the experiments. We postulate that this sinusoidal behavior is a response to gravity waves propagating above Puerto Rico. Nearly simultaneous data from two nearby stations show that GPS signals were modified by variations in total electron content (TEC) indicating the presence of traveling ionospheric disturbances (TIDs). The December 26 experiments were conducted about a day after an M W = 9.2 earthquake launched tsunami waves first across the Indian, then into the Atlantic and Pacific Oceans. We suggest that coupling at the tsunami sea-air interface launched gravity waves that propagated for great distances beneath the mesopause. GPS data recorded TEC variation in Asia, Europe, and the Caribbean, suggesting that TIDs were induced on a global scale at the wake of tsunami-launched gravity waves. Energy from imperfectly ducted gravity waves leaked into the ionosphere, partially over Puerto Rico. The wind-velocity field of these gravity waves caused local ionospheric plasma to rise, seeding bottomside irregularities via the generalized Rayleigh-Taylor instability.

While plasticity is typically associated with persistent modifications of synaptic strengths, recent studies indicated that modulations of dendritic excitability may form the other part of the engram and dynamically affect computational processing and output of neuronal circuits. However it remains unknown whether modulation of dendritic excitability is controlled by synaptic changes or whether it can be distinct from them. Here we report the first observation of the induction of a persistent plastic decrease in dendritic excitability decoupled from synaptic stimulation, which is localized and purely activity-based. In rats this local plasticity decrease is conferred by CamKII mediated phosphorylation of A-type potassium channels upon interaction of a back propagating action potential (bAP) with dendritic depolarization.

Brownian motion of slender particles near a boundary is ubiquitous in biological systems and in nanomaterial assembly, but the complex hydrodynamic interaction in those systems is still poorly understood. Here, we report experimental and computational studies of the Brownian motion of silicon nanowires tethered on a substrate. An optical interference method enabled direct observation of microscopic rotations of the slender bodies in three dimensions with high angular and temporal resolutions. This quantitative observation revealed anisotropic and angle-dependent hydrodynamic wall effects: rotational diffusivity in inclined and azimuth directions follows different power laws as a function of the length, ∼ L(-2.5) and ∼ L(-3), respectively, and is more hindered for smaller inclined angles. In parallel, we developed an implicit simulation technique that takes the complex wire-wall hydrodynamic interactions into account efficiently, the result of which agreed well with the experimentally observed angle-dependent diffusion. The demonstrated techniques provide a platform for studying the microrheology of soft condensed matters, such as colloidal and biological systems near interfaces, and exploring the optimal self-assembly conditions of nanostructures.

[1] The Naval transmitter, code-named NAU, in Puerto Rico emits radio waves at a power and frequency of 100 kW and 40.75 kHz, respectively. The NAU-generated 40.75 kHz whistler-mode waves are intense enough to excite lower hybrid waves and zero-frequency field-aligned ionospheric irregularities over Arecibo. It is proposed that NAU is responsible for causing the enhanced plasma lines, detected by the Arecibo 430 MHz radar in the nighttime ionosphere F region, in the presence of spread F events. The lower hybrid waves, generated in a broad range of altitudes at the wake of 40.75 kHz whistler-mode waves, have a single frequency of 40.75 kHz but with a spectrum of wavelengths. They can effectively accelerate electrons continuously along the Earth's magnetic field with energies from a fraction of 1 eV to 10 eV. These energetic streaming electrons, when detected by the Arecibo 430 MHz radar, give rise to enhanced plasma lines with a frequency spectrum of $3.25-4.75 MHz.

[1] We examine possible correlations between occurrences of nighttime E-region plasma line (PL) enhancements over Arecibo and 40.75 kHz NAU emissions. On the night of January 1 -2, 2006, the experiments were conducted from 22:00 to 6:00 local time (LT). NAU transmitter was initially turned off until 01:45 LT, when continuous operations resumed for the remainder of the experiments. Enhanced PL events lasting <10 s had central frequencies and bandwidths of about 2.5 and 1.5 MHz, respectively, indicating that Arecibo radar detected 2.3 to 8.5 eV suprathermal electrons streaming along geomagnetic fields. The rate of PL event detections increased by a factor of 2.8 after NAU turn-on. We suggest that 40.75 kHz radiation sporadically leaked though local ionosphere, probably abetted by field-aligned irregularities. The radiation propagated in whistler mode into the L = 1.35 inner radiation belt where gyroresonant interactions with trapped 390 keV electrons increased the precipitation rate. Citation: Pradipta, R