Microcircuits in visual cortex

The microcircuitry of the neocortex is bewildering in its anatomical detail, but seen through the filters of physiology, some simple circuits have been suggested. Intensive investigations of the cortical representation of orientation, however, show how difficult it is to achieve any consensus on what the circuits are, how they develop, and how they work. New developments in modeling allied with powerful experimental tools are changing this. Experimental work combining optical imaging with anatomy and physiology has revealed a rich local cortical circuitry. Whereas older models of cortical circuits have concentrated on simple 'feedforward' circuits, newer theoretical work has explored more the role of the recurrent cortical circuits, which are more realistic representations of the actual circuits and are computationally richer.     

Molecular Filters for Noise Reduction

Living systems are inherently stochastic and operate in a noisy environment, yet despite all these uncertainties, they perform their functions in a surprisingly reliable way. The biochemical mechanisms used by natural systems to tolerate and control noise are still not fully understood, and this issue also limits our capacity to engineer reliable, quantitative synthetic biological circuits. We study how representative models of biochemical systems propagate and attenuate noise, accounting for intrinsic as well as extrinsic noise. We investigate three molecular noise-filtering mechanisms, study their noise-reduction capabilities and limitations, and show that nonlinear dynamics such as complex formation are necessary for efficient noise reduction. We further suggest that the derived molecular filters are widespread in gene expression and regulation and, particularly, that microRNAs can serve as such noise filters. To our knowledge, our results provide new insight into how biochemical networks control noise and could be useful to build robust synthetic circuits.     

Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors

The engineering of synthetic gene networks has mostly relied on the assembly of few characterized regulatory elements using rational design principles. It is of outmost importance to analyze the scalability and limits of such a design workflow. To analyze the design capabilities of libraries of regulatory elements, we have developed the first automated design approach that combines such elements to search the genotype space associated to a given phenotypic behavior. Herein, we calculated the designability of dynamical functions obtained from circuits assembled with a given genetic library. By designing circuits working as amplitude filters, pulse counters and oscillators, we could infer new mechanisms for such behaviors. We also highlighted the hierarchical design and the optimization of the interface between devices. We dissected the functional diversity of a constrained library and we found that even such libraries can provide a rich variety of behaviors. We also found that intrinsic noise slightly reduces the designability of digital circuits, but it increases the designability of oscillators. Finally, we analyzed the robust design as a strategy to counteract the evolvability and noise in gene expression of the engineered circuits within a cellular background, obtaining mechanisms for robustness through non-linear negative feedback loops.     

Light-controlled synthetic gene circuits

Highly complex synthetic gene circuits have been engineered in living organisms to develop systems with new biological properties. A precise trigger to activate or deactivate these complex systems is desired in order to tightly control different parts of a synthetic or natural network. Light represents an excellent tool to achieve this goal as it can be regulated in timing, location, intensity, and wavelength, which allows for precise spatiotemporal control over genetic circuits. Recently, light has been used as a trigger to control the biological function of small molecules, oligonucleotides, and proteins involved as parts in gene circuits. Light activation has enabled the construction of unique systems in living organisms such as band-pass filters and edge-detectors in bacterial cells. Additionally, light also allows for the regulation of intermediate steps of complex dynamic pathways in mammalian cells such as those involved in kinase networks. Herein we describe recent advancements in the area of light-controlled synthetic networks.     

Color perception is mediated by a plastic neural mechanism that is adjustable in adults

An intensely debated issue concerning visual-experience-dependent neural plasticity is whether experience is required only to maintain function or whether information from experience is used actively, relieving the necessity to hard-wire all connections and allowing adaptive adjustments. Here, an active role for experience is demonstrated in circuits for color vision. Chromatic experience was altered using colored filters. Over days there was a shift in color perception, as measured by the wavelength of unique yellow, which persisted 1-2 weeks after the filters were discontinued. Moreover, color-deficient adults were shown to have altered weightings of inputs to chromatic channels, demonstrating a large neural adjustment to their inherited photopigment defect. Thus, a neural normalization mechanism for color perception, determined by visual experience, operates to compensate for large genetic differences in retinal architecture and for changes in chromatic environment.     

Systematic Computation of Nonlinear Cellular and Molecular Dynamics with Low-Power CytoMimetic Circuits: A Simulation Study

This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented.     

Parallel processing in the mammalian retina

Our eyes send different 'images' of the outside world to the brain - an image of contours (line drawing), a colour image (watercolour painting) or an image of moving objects (movie). This is commonly referred to as parallel processing, and starts as early as the first synapse of the retina, the cone pedicle. Here, the molecular composition of the transmitter receptors of the postsynaptic neurons defines which images are transferred to the inner retina. Within the second synaptic layer - the inner plexiform layer - circuits that involve complex inhibitory and excitatory interactions represent filters that select 'what the eye tells the brain'.     

A Compact Nanoplasmonics Filter and Intersection Structure Based on Utilizing a Slot Cavity and a Fabry–Perot Resonator

By combining a Fabry–Perot (FP) cavity with a slot cavity, a compact filter structure is proposed. The peak resonance wavelength is determined by applying the FP resonance condition of the FP cavity. The relationship between filtering wavelength and cavity parameters is investigated. The results show that the filtering wavelength can be manipulated by changing the nanocavities' parameters. By using the finite difference time domain method, the theoretical predictions are confirmed. An intersection structure for nanoplasmonic waveguides is proposed and designed by utilizing two perpendicular filters. In addition to having compact dimensions, the proposed arrangement provides higher throughput and low cross talk. The proposed structure can be useful for designing compact integrated nanoplasmonic circuits.     

Focusing on optic tectum circuitry through the lens of genetics

The visual pathway is tasked with processing incoming signals from the retina and converting this information into adaptive behavior. Recent studies of the larval zebrafish tectum have begun to clarify how the 'micro-circuitry' of this highly organized midbrain structure filters visual input, which arrives in the superficial layers and directs motor output through efferent projections from its deep layers. The new emphasis has been on the specific function of neuronal cell types, which can now be reproducibly labeled, imaged and manipulated using genetic and optical techniques. Here, we discuss recent advances and emerging experimental approaches for studying tectal circuits as models for visual processing and sensorimotor transformation by the vertebrate brain.     

Trade-offs and Noise Tolerance in Signal Detection by Genetic Circuits

Genetic circuits can implement elaborated tasks of amplitude or frequency signal detection. What type of constraints could circuits experience in the performance of these tasks, and how are they affected by molecular noise? Here, we consider a simple detection process–a signal acting on a two-component module–to analyze these issues. We show that the presence of a feedback interaction in the detection module imposes a trade-off on amplitude and frequency detection, whose intensity depends on feedback strength. A direct interaction between the signal and the output species, in a type of feed-forward loop architecture, greatly modifies these trade-offs. Indeed, we observe that coherent feed-forward loops can act simultaneously as good frequency and amplitude noise-tolerant detectors. Alternatively, incoherent feed-forward loop structures can work as high-pass filters improving high frequency detection, and reaching noise tolerance by means of noise filtering. Analysis of experimental data from several specific coherent and incoherent feed-forward loops shows that these properties can be realized in a natural context. Overall, our results emphasize the limits imposed by circuit structure on its characteristic stimulus response, the functional plasticity of coherent feed-forward loops, and the seemingly paradoxical advantage of improving signal detection with noisy circuit components.     

Tunable,Mid-Infrared Ultra-Narrowband Filtering Effect Induced by Two Coplanar Graphene Strips

The two coplanar graphene strips coupling system supported on substrates is proposed and constructed on a monolayer graphene by spatially varying gate voltages. It is investigated numerically by using the finite-difference time-domain method. Simulation results reveal that despite of no traditional ring, disk, and rectangular geometry resonators used usually in metallic plasmonic filters, this structure based on the edge mode propagation exhibits an original, ultra-narrowband band-stop filtering effect in the mid-infrared region. This filtering effect results from the novel side-coupled resonator formed by the parallel graphene strips. The transmission spectrum is tuned and modified not only by engineering the locations of gate voltages without re-fabricating structures but also via changing substrates. Simulation results are consistent with the theoretical analysis. Our studies hence support the fabrication of ultra-compact planar plasmonic devices in nano-integrated circuits.     

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.     

Tunable Slow Light in Graphene Metamaterial in a Broad Terahertz Range

A graphene-based metamaterial with tunable electromagnetically induced transparency is numerically studied in this paper. The proposed structure consists of a graphene layer composed of H shape between two cut wires, by breaking symmetry can control EIT-like effects and by increasing the asymmetry in the structure has strong coupling between elements. It is important that the peak frequency of transmission window can be dynamically controlled over a broad frequency range by varying the chemical potential of graphene layer. The results show that high refractive index sensitivity and figure of merit can be achieved in asymmetrical structures which is good for sensing applications. We calculated the group delay and the results show we can control the group velocity by varying the S parameter in asymmetrical structure. The characteristics of our system indicate important potential applications in integrated optical circuits such as optical storage, ultrafast plasmonic switches, high performance filters, and slow-light devices.     

Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity

Interneurons are critical for neuronal circuit function, but how their dendritic morphologies and membrane properties influence information flow within neuronal circuits is largely unknown. We studied the spatiotemporal profile of synaptic integration and short-term plasticity in dendrites of mature cerebellar stellate cells by combining two-photon guided electrical stimulation, glutamate uncaging, electron microscopy, and modeling. Synaptic activation within thin (0.4?μm) dendrites produced somatic responses that became smaller and slower with increasing distance from the soma, sublinear subthreshold input-output relationships, and a somatodendritic gradient of short-term plasticity. Unlike most studies showing that neurons employ active dendritic mechanisms, we found that passive cable properties of thin dendrites determine the sublinear integration and plasticity gradient, which both result from large?dendritic depolarizations that reduce synaptic driving force. These integrative properties allow stellate cells to act as spatiotemporal filters of synaptic input patterns, thereby biasing their output in favor of sparse presynaptic activity.     

Modification of standard CMOS technology for cell-based biosensors

We present an electrode based on complementary metal oxide semiconductor (CMOS) technology that can be made fully biocompatible and chemically inert using a simple, low-cost and non-specialised process. Since these devices are based on ubiquitous CMOS technology, the integrated circuits can be readily developed to include appropriate amplifiers, filters and wireless subsystems, thus reducing the complexity and cost of external systems. The unprocessed CMOS aluminium electrodes are modified using anodisation and plating techniques which do not require intricate and expensive semiconductor processing equipment and can be performed on the bench-top as a clean-room environment is not required. The resulting transducers are able to detect both the fast electrical activity of neurons and the slow changes in impedance of growing and dividing cells. By using standard semiconductor fabrication techniques and well-established technologies, the approach can form the basis of cell-based biosensors and transducers for high throughput drug discovery assays, neuroprosthetics and as a basic research tool in biosciences. The technology is equally applicable to other biosensors that require noble metal or nanoporous microelectrodes.     

Neuromorphic hardware databases for exploring structure-function relationships in the brain.

Neuromorphic hardware is the term used to describe full custom-designed integrated circuits, or silicon ''chips'', that are the product of neuromorphic engineering--a methodology for the synthesis of biologically inspired elements and systems, such as individual neurons, retinae, cochleas, oculomotor systems and central pattern generators. We focus on the implementation of neurons and networks of neurons, designed to illuminate structure-function relationships. Neuromorphic hardware can be constructed with either digital or analogue circuitry or with mixed-signal circuitry--a hybrid of the two. Currently, most examples of this type of hardware are constructed using analogue circuits, in complementary metal-oxide-semiconductor technology. The correspondence between these circuits and neurons, or networks of neurons, can exist at a number of levels. At the lowest level, this correspondence is between membrane ion channels and field-effect transistors. At higher levels, the correspondence is between whole conductances and firing behaviour, and filters and amplifiers, devices found in conventional integrated circuit design. Similarly, neuromorphic engineers can choose to design Hodgkin-Huxley model neurons, or reduced models, such as integrate-and-fire neurons. In addition to the choice of level, there is also choice within the design technique itself; for example, resistive and capacitive properties of the neuronal membrane can be constructed with extrinsic devices, or using the intrinsic properties of the materials from which the transistors themselves are composed. So, silicon neurons can be built, with dendritic, somatic and axonal structures, and endowed with ionic, synaptic and morphological properties. Examples of the structure-function relationships already explored using neuromorphic hardware include correlation detection and direction selectivity. Establishing a database for this hardware is valuable for two reasons: first, independently of neuroscientific motivations, the field of neuromorphic engineering would benefit greatly from a resource in which circuit designs could be stored in a form appropriate for reuse and re-fabrication. Analogue designers would benefit particularly from such a database, as there are no equivalents to the algorithmic design methods available to designers of digital circuits. Second, and more importantly for the purpose of this theme issue, is the possibility of a database of silicon neuron designs replicating specific neuronal types and morphologies. In the future, it may be possible to use an automated process to translate morphometric data directly into circuit design compatible formats. The question that needs to be addressed is: what could a neuromorphic hardware database contribute to the wider neuroscientific community that a conventional database could not? One answer is that neuromorphic hardware is expected to provide analogue sensory-motor systems for interfacing the computational power of symbolic, digital systems with the external, analogue environment. It is also expected to contribute to ongoing work in neural-silicon interfaces and prosthetics. Finally, there is a possibility that the use of evolving circuits, using reconfigurable hardware and genetic algorithms, will create an explosion in the number of designs available to the neuroscience community. All this creates the need for a database to be established, and it would be advantageous to set about this while the field is relatively young. This paper outlines a framework for the construction of a neuromorphic hardware database, for use in the biological exploration of structure-function relationships.     

Eigenschaften diskreter Ortsfilter

Summary Properties of discrete spatial filters are investigated. By introducing rectangular or oblique coordinates it is possible to design filters in a quadratic or hexagonal raster. The design of low-pass, high-pass and band-pass filters is shown. Their properties are evaluated by computing an example; different filters are compared. It is possible to design arbitrary filters; however, there are limitations due to quantization error and approximation of filters by a necessarily finite (and small) number of elements.     

Fungal colonization of air filters for use in heating,ventilating, and air conditioning (HVAC) systems

Summary New and used cellulosic air filters for HVAC systems including those treated with antimicrobials were suspended in vessels with a range of relative humidities (55–99%) and containing non-sterile potting soil which stimulates fungal growth. Most filters yielded fungi prior to suspension in the chambers but only two of 14 nontreated filters demonstrated fungal colonization following use in HVAC systems. Filters treated with antimicrobials, particularly a phosphated amine complex, demonstrated markedly less fungal colonization than nontreated filters. In comparison with nontreated cellulosic filters, fungal colonization of antimicrobial-treated cellulosic filters was selective and delayed.     

Growth of Streptococcal Protoplasts and L-Colonies on Membrane Filters

Membrane filters (Millipore Corp.; pore sizes 1.2 to 0.22 mum) were placed on the surface of L-phase growth medium solidified with agar. The filter and the surrounding medium were inoculated with either protoplasts or stable broth-grown L-phase variants obtained from Streptococcus faecium strain F24. The L-phase inoculum gave rise to viable L-colonies on the filters and on the medium, whereas protoplasts gave colony formation only on the medium. However, when the Millipore filters were covered by a layer of solid L-phase medium, 75 mum or greater in depth, before inoculation with protoplasts, colony formation resulted but with atypical morphology. In contrast, inoculation of protoplasts on Nuclepore and Sartorius membrane filters did give rise to L-colonies on the surface and underneath the filters after 2 days of incubation at 37 C. Submicroscopic, viable L-phase elements produced during colony formation were capable of passing through membrane filters with pore channels as small as 0.22 mum; these elements required transfer from underneath the filters to fresh agar medium in order to develop into L-phase colonies. Membrane filters were also placed on the surface of L-phase growth medium solidified with gelatin. Inoculation of the filters and surrounding medium with a lysozyme-prepared protoplast suspension gave rise to streptococci on the surface of the filters and on the medium. However, inoculation with the stable broth-grown L-phase variants gave rise to atypical colonies on the medium and only small patches of abortive growth on the filters.     

Use of nuclepore filters for counting bacteria by fluorescence microscopy.

Polycarbonate Nuclepore filters are better than cellulose filters for the direct counting of bacteria because they have uniform pore size and a flat surface that retains all of the bacteria on top of the filter. Although cellulose filters also retain all of the bacteria, many are trapped inside the filter where they cannot be counted. Before use, the Nuclepore filters must be dyed with irgalan black to eliminate autofluorescence. Direct counts of bacteria in lake and ocean waters are twice as high with Nuclepore filters as with cellulose filters.