Stimulus Discrimination in Cerebellar Purkinje Neurons

Cerebellar Purkinje neurons fire spontaneously in the absence of synaptic input. Overlaid on this intrinsic activity, excitatory input from parallel fibres can add simple spikes to the output train, whereas inhibitory input from interneurons can introduce pauses. These and other influences lead to an irregular spike train output in Purkinje neurons in vitro and in vivo, supplying a variable inhibitory drive to deep cerebellar nuclear neurons. From a computational perspective, this variability raises some questions, as individual spikes induced by excitatory inputs are indistinguishable from intrinsic firing activity. Although bursts of high-frequency excitatory input could be discriminated unambiguously from background activity, granule neurons are known to fire in vivo over a wide range of frequencies. This would mean that much of the sensory information relayed through the cerebellar cortex would be lost within the random variation in background activity. We speculated that alternative mechanisms for signal discrimination may exist, and sought to identify characteristic motifs within the sequence of spikes that followed stimulation events. We found that under certain conditions, parallel fibre stimulation could reliably add a “couplet” of spikes with an unusually short interspike interval to the output train. Therefore, despite representing a small fraction of the total number of spikes, these signals can be reliably discriminated from background firing on a moment-to-moment basis, and could result in a differential downstream response

Sectionality or Why Section Determines Grades: an Exploration of Engineering Core Course Section Grades using a Hierarchical Linear Model and the Multiple-Institution Database for Investigating Engineering Longitudinal Development

Grades, how they are earned, and the institutional impetuses that drive them, are an issue of central importance in the engineering discipline. (1-4) How grades are earned, how different institutions address grades and grade inequities, how instructional practices and policies affect grades, and other grading notions have been studied widely in engineering education. (5-8) The effect of faculty on student grades, while studied, (9) has not been probed as extensively within engineering education using a hierarchical linear model (HLM).One of the great, open questions in engineering education is whether or not the section makes a difference in a student’s grade. In other words, the effect of sectionality on grades to a large extent is unknown. Sectionality combines instructor effects, effects related to time-of-day of instruction, effects related to any tendency for students to coordinate their enrollment, and other effects. Experience and anecdotal evidence suggest that sectionality affects grades, but large-scale empirical studies of this phenomenon do not exist. Due to the inherent structured nature between course sections and students, standard linear regression models do not offer a robust solution to probing longitudinal systems containing multilevel variables. Hierarchical Linear Models (HLMs) provide a robust solution to studying nested or hierarchical systems when compared with standard regression techniques. We constructed a simple HLM to probe inter-section and intra-section variability in grades within the Multiple Institution Database for Investigating Engineering Longitudinal Development (MIDFIELD) by the calculation of intraclass correlation coefficient (ICCs). (10, 11) We then examined grades from three sets of courses endemic to the first year engineering experience: the first chemistry course; the first calculus course; and the first physics course. Our preliminary results indicate that the choice of a HLM to analyze our longitudinal database is correct due to strong variability in grades explained by the high intraclass correlation coefficient (ICC) for most of our MIDFIELD institutions across all three course types analyzed

Probabilistic encoding of stimulus strength in astrocyte global calcium signals

Astrocyte calcium signals can range in size from subcellular microdomains to waves that spread through the whole cell (and into connected cells). The differential roles of such local or global calcium signaling are under intense investigation, but the mechanisms by which local signals evolve into global signals in astrocytes are not well understood, nor are the computational rules by which physiological stimuli are transduced into a global signal. To investigate these questions, we transiently applied receptor agonists linked to calcium signaling to primary cultures of cerebellar astrocytes. Astrocytes repetitively tested with the same stimulus responded with global signals intermittently, indicating that each stimulus had a defined probability for triggering a response. The response probability varied between agonists, increased with agonist concentration, and could be positively and negatively modulated by crosstalk with other signaling pathways. To better understand the processes determining the evolution of a global signal, we recorded subcellular calcium “puffs” throughout the whole cell during stimulation. The key requirement for puffs to trigger a global calcium wave following receptor activation appeared to be the synchronous release of calcium from three or more sites, rather than an increasing calcium load accumulating in the cytosol due to increased puff size, amplitude, or frequency. These results suggest that the concentration of transient stimuli will be encoded into a probability of generating a global calcium response, determined by the likelihood of synchronous release from multiple subcellular sites

Photochromic molecular implementations of universal computation

Unconventional computing is an area of research in which novel materials and paradigms are utilised to implement computation. Previously we have demonstrated how registers, logic gates and logic circuits can be implemented, unconventionally, with a biocompatible molecular switch, NitroBIPS, embedded in a polymer matrix. NitroBIPS and related molecules have been shown elsewhere to be capable of modifying many biological processes in a manner that is dependent on its molecular form. Thus, one possible application of this type of unconventional computing is to embed computational processes into biological systems. Here we expand on our earlier proof-of-principle work and demonstrate that universal computation can be implemented using NitroBIPS. We have previously shown that spatially localised computational elements, including registers and logic gates, can be produced. We explain how parallel registers can be implemented, then demonstrate an application of parallel registers in the form of Turing machine tapes, and demonstrate both parallel registers and logic circuits in the form of elementary cellular automata. The Turing machines and elementary cellular automata utilise the same samples and same hardware to implement their registers, logic gates and logic circuits; and both represent examples of universal computing paradigms. This shows that homogenous photochromic computational devices can be dynamically repurposed without invasive reconfiguration. The result represents an important, necessary step towards demonstrating the general feasibility of interfacial computation embedded in biological systems or other unconventional materials and environments

Reconfigurable ferromagnetic liquid droplets.

Solid ferromagnetic materials are rigid in shape and cannot be reconfigured. Ferrofluids, although reconfigurable, are paramagnetic at room temperature and lose their magnetization when the applied magnetic field is removed. Here, we show a reversible paramagnetic-to-ferromagnetic transformation of ferrofluid droplets by the jamming of a monolayer of magnetic nanoparticles assembled at the water-oil interface. These ferromagnetic liquid droplets exhibit a finite coercivity and remanent magnetization. They can be easily reconfigured into different shapes while preserving the magnetic properties of solid ferromagnets with classic north-south dipole interactions. Their translational and rotational motions can be actuated remotely and precisely by an external magnetic field, inspiring studies on active matter, energy-dissipative assemblies, and programmable liquid constructs

Surface plasmon resonance imaging of excitable cells

Surface plasmons (SPs) are surface charge density oscillations occuring at a metal/dieletric interface and are highly sensitive to refractive index variations adjacent to the surface. This sensitivity has been exploited successfully for chemical and biological assays. In these systems, a surface plasmon resonance (SPR)-based sensor detects temporal variations in the refractive index at a point. SPR has also been used in imaging systems where the spatial variations of refractive index in the sample provide the contrast mechanism. SPR imaging systems using high numerical aperture (NA) objective lenses have been designed to image adherent live cells with high magnification and near-diffraction limited spatial resolution. Addressing research questions in cell physiology and pharmacology often requires the development of a multimodal microscope where complementary information can be obtained.In this paper, we present the development of a multimodal microscope that combines SPR imaging with a number of additional imaging modalities including bright-field, epifluorescence, total internal reflection microscopy and SPR fluorescence microscopy. We used a high NA objective lens for SPR and TIR microscopy and the platform has been used to image live cell cultures demonstrating both fluorescent and label-free techniques. Both the SPR and TIR imaging systems feature a wide field of view (~300 µm) that allows measurements from multiple cells whilst maintaining a resolution sufficient to image fine cellular processes. The capability of the platform to perform label-free functional imaging of living cells was demonstrated by imaging the spatial variations in contractions from stem cell-derived cardiomyocytes. This technique shows promise for non-invasive imaging of cultured cells over very long periods of time during development

Multivariate analysis of 3D ToF-SIMS images: method validation and application to cultured neuronal networks

Advanced data analysis tools are crucial for the application of ToF-SIMS analysis to biological samples. Here, we demonstrate that by using a training set approach principal components analysis (PCA) can be performed on large 3D ToF-SIMS images of neuronal cell cultures. The method readily provides access to sample component information and significantly improves the images’ signal-to-noise ratio (SNR)

A reconfigurable real-time compressive-sampling camera for biological applications

Many applications in biology, such as long-term functional imaging of neural and cardiac systems, require continuous high-speed imaging. This is typically not possible, however, using commercially available systems. The frame rate and the recording time of high-speed cameras are limited by the digitization rate and the capacity of on-camera memory. Further restrictions are often imposed by the limited bandwidth of the data link to the host computer. Even if the system bandwidth is not a limiting factor, continuous high-speed acquisition results in very large volumes of data that are difficult to handle, particularly when real-time analysis is required. In response to this issue many cameras allow a predetermined, rectangular region of interest (ROI) to be sampled, however this approach lacks flexibility and is blind to the image region outside of the ROI. We have addressed this problem by building a camera system using a randomly-addressable CMOS sensor. The camera has a low bandwidth, but is able to capture continuous high-speed images of an arbitrarily defined ROI, using most of the available bandwidth, while simultaneously acquiring low-speed, full frame images using the remaining bandwidth. In addition, the camera is able to use the full-frame information to recalculate the positions of targets and update the high-speed ROIs without interrupting acquisition. In this way the camera is capable of imaging moving targets at high-speed while simultaneously imaging the whole frame at a lower speed. We have used this camera system to monitor the heartbeat and blood cell flow of a water flea (Daphnia) at frame rates in excess of 1500 fps

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus

Identification of MIR390a precursor processing defective mutants in Arabidopsis by direct genome sequencing

Transacting siRNA (tasiRNA) biogenesis in Arabidopsis is initiated by microRNA (miRNA) –guided cleavage of primary transcripts. In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)– miR390 complexes interact with primary transcripts at two sites, resulting in recruitment of RNA-DEPENDENT RNA POLYMERASE6 for dsRNA biosynthesis. An extensive screen for Arabidopsis mutants with specific defects in TAS3 tasiRNA biogenesis or function was done. This yielded numerous ago7 mutants, one dcl4 mutant, and two mutants that accumulated low levels of miR390. A direct genome sequencing-based approach to both map and rapidly identify one of the latter mutant alleles was developed. This revealed a G-to-A point mutation (mir390a-1) that was calculated to stabilize a relatively nonpaired region near the base of the MIR390a foldback, resulting in misprocessing of the miR390/ miR390* duplex and subsequent reduced TAS3 tasiRNA levels. Directed substitutions, as well as analysis of variation at paralogous miR390-generating loci (MIR390a and MIR390b), indicated that base pair properties and nucleotide identity within a region 4–6 bases below the miR390/miR390* duplex region contributed to the efficiency and accuracy of precursor processing